combined annual report (version 1.1) bemp 2012-2017 v1.1.pdf · combined annual report (version...

BROADSCALE ENVIRONMENTAL MONITORING PROGRAM

D’Entrecasteaux Channel and Huon Marine Farming

Development Plan Sites

COMBINED ANNUAL REPORT (VERSION 1.1) 2012/13-2016/17

November 2017

Report to: TSGA

Prepared by: AQUENAL PTY LTD

A Q U E N A L

www.aquenal.com.au

Aquenal Pty Ltd BEMP Combined report 2012/13-2016-17

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Document Control Date Company Detail Version

23/11/2017 Aquenal Pty Ltd Draft report 1.0

20/4/2018 Aquenal Pty Ltd Editorial changes 1.1

Document Distribution

Date Company Document Type

Version Copies

23/11/2017 TSGA Electronic 1.0 1

23/11/2017 Tassal Electronic 1.0 1

23/11/2017 Huon Aquaculture Electronic 1.0 1

23/11/2017 Marine Farming Branch Electronic 1.0 1

23/11/2017 EPA Electronic 1.0 1

20/4/2018 TSGA Electronic 1.1 1

REPORT CITATION: Broadscale Environmental Monitoring Program – D’Entrecasteaux Channel and Huon Marine Farming Development Plan Sites – Combined Annual Report 2012/13-2016/17, November 2017, Report to TSGA, 110pp.

COPYRIGHT: The concepts and information contained in this document are the property of

Aquenal Pty Ltd. Use or copying of this document in whole or in part without the written

permission of Aquenal Pty Ltd constitutes an infringement of copyright.

DISCLAIMER: This report has been prepared on behalf of and for the exclusive use of Aquenal Pty

Ltd’s client and is subject to and issued in connection with the provisions of the agreement

between Aquenal Pty Ltd and its Client. Aquenal Pty Ltd accepts no liability or responsibility

whatsoever for or in respect of any use of or reliance upon this report by any third party.


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Executive Summary The Broadscale Environmental Monitoring Program (BEMP) was initiated in 2009 to provide knowledge and information on ecosystem function in the D’Entrecasteaux Channel and Huon Estuary. The objective of the program was to document broad scale spatial and temporal trends for key environmental parameters, allowing assessment of the environmental effects of finfish aquaculture in the region. The sampling specifications for this project are included in Schedule 3BEMP to marine farming licences for finfish growing operations located within the D’Entrecasteaux Channel Marine Farm Development Plan (MFDP) and Huon/Port Esperance MFDP areas. The BEMP program includes assessment of water and sediment health at a broad scale level across the study area and was largely structured around recommendations of previous studies undertaken in the region. Sediment sampling includes benthic infauna, stable isotopes, particle size, visual assessment, redox analysis and sulphide measurements. Visual assessment, redox and sulphide analysis is carried out each year, while analysis of benthic infauna, stable isotopes and particle size is undertaken every 4 years. In the intervening years these samples are collected, preserved and retained. Assessment of the samples retained from the intervening years may be required where sediment geo-chemistry parameters (e.g. redox, sulphide) and/or the 4-yearly benthic faunal parameters are triggered. Water quality analytes include physico-chemical parameters (temperature, dissolved oxygen, salinity), nutrients (dissolved nutrients: ammonia, nitrate, phosphate, silicate, total nutrients: total nitrogen, total phosphorous), chlorophyll a and phytoplankton species counts. Water quality sampling is undertaken monthly from May to January and fortnightly from February to April. A total of 15 sites are included in the monitoring program; including 9 sites in the D’Entrecasteaux Channel MFDP, 5 sites in the Huon River/Port Esperance MFDP’s and a control site at Recherche Bay. This current report includes an assessment of water quality and sediment sampling events beginning in March 2012 and ending in February 2017. This equated to 5 BEMP reporting years including 2012/13, 2013/14, 2014/15, 2015/16 and 2016/17. The BEMP reporting period is based upon rolling 12 month periods beginning in March and ending in February the following year. A summary of results during the reporting period is provided below. Data summary – sediment health Analysis of benthic infauna samples collected in 2009 and 2013 showed no evidence of a major shift in species composition or organic enrichment, with community composition very similar between surveys. The only potential indicator of a change in ecosystem condition was an increase in abundance of the introduced bivalve species Varicorbula gibba and Theora lubrica that were recorded at some sites. Since only two sets of faunal data have been examined it is not clear whether this is an increasing trend or part of a natural cycle. Future benthic analyses of 2017 data will enable improved assessment of introduced species patterns. Annual visual assessment of sediment cores across the survey period in the reporting period (i.e. 2012-2016) showed no major changes in sediment characteristics since the inception of the monitoring program. Patterns of redox potential also appeared relatively consistent for all survey years. Redox values observed in 2016 were within the range of values observed in the previous years, and there was no evidence of a decrease in redox potential for any of the monitoring sites. Organic enrichment is typically indicated by redox values < 0 mV and there has been no such evidence through the course of the monitoring program. At most monitoring sites, average redox values have consistently exceeded 100 mV, these levels are indicative of unimpacted sediments.


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Sulphide levels have remained very low across all sites and survey events, with the majority of readings close to zero or not detectable. While still at low levels, sulphide levels tended to be slightly higher relative to other sites at B10, B13 and B15. No site has a sulphide concentration exceeding 100 µM, suggesting that there is no evidence of broad scale organic enrichment across the survey area. Particle size and stable isotope analysis were analysed in 2009 and 2013. For particle size analysis, patterns of sediment grain size were comparable between years and reflect the variation in wave exposure and current strength across the survey area. For stable isotope analyses, C:N ratios and 13C/15C results were comparable between the 2009 and 2013 surveys. The stable isotope analyses showed no evidence of broad scale impacts attributable to fish farming in the study area. Data covering a greater span of sampling years will be important to determine levels of stable isotope variation for the D’Entrecasteaux Channel and Huon Estuary. Overall, based on the benthic infauna and sediment chemistry parameters considered (visual assessment, redox, sulphide, particle size, stable isotopes) for the reporting period 2012/13-2016/2017, there were no consistent trends considered strong evidence of organic enrichment at the broad scale monitoring sites sampled under the BEMP program. Data summary – water quality Physico-chemical parameters (temperature, dissolved oxygen, salinity) were generally comparable between survey years. For dissolved oxygen, consistent seasonal patterns were evident, particularly in bottom waters, with oxygen concentration reaching minimum levels in late summer and autumn. Patterns of dissolved oxygen were very similar for D’Entrecasteaux Channel sites and the control site. Huon River sites, in contrast, showed considerable variation. Bottom water dissolved oxygen concentrations tended to decrease with increasing distance upstream, with lowest average bottom water dissolved oxygen measured at site 13. Patterns of dissolved oxygen across the reporting period were generally comparable to earlier sampling years. For most nutrients (i.e. nitrate, phosphate, silicate, total nitrogen, total phosphorous), concentrations measured in the 2012/13-2016/17 reporting period were within the range recorded in previous sampling years and there was no evidence of broad scale changes in water quality characteristics. Patterns of ammonia concentration within the 2012/13-2016/17 reporting period were also generally within the range recorded during previous sampling years at most sites, with peaks in bottom water ammonia largely driven by Huon sites (sites 10-14). However, at some sites there was a trend of higher ammonia concentrations in the latter part of the reporting period (2014/15 onwards). These slightly higher ammonia levels were most evident at sites 8 and 9 in the D’Entrecasteaux Channel and site 10 in the Huon. Average ammonia levels recorded during December 2014 were also among the highest mean values recorded since the inception of the monitoring program (mean bottom water ammonia concentration 0.18 mg-N/L). Chlorophyll a patterns were characterised by peaks in spring and autumn in most years, with seasonal minimums occurring in winter each year. The highest average chlorophyll a concentration during the 2012/13-2016/17 reporting period occurred in September 2015, when chlorophyll a averaged 3.5 mg/m3 across all sites. There was no evidence of increasing chlorophyll a concentrations over the reporting period, nor was there evidence that the frequency and/or magnitude of bloom events has changed. There was also no evidence of increasing abundance of harmful phytoplankton species during the reporting period.


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Proposed trigger levels Proposed baseline values and trigger levels were established by Thompson et al. (2008) following water quality and sediment surveys in the D’Entrecasteaux Channel and Huon Estuary. The trigger values provide a framework for developing management responses based on the extent a particular parameter exceeds the trigger value. They also take into account the various risks to ecological structure and function. It is important to note that the proposed trigger levels are not statutory limits and their purpose was to inform regulatory management of the industry. Trigger level assessment categories include level 1 (low risk), level 2 (moderate risk) and level 3 (high risk) categories. It is expected that these guideline values will be reviewed by the EPA following recent changes to aquaculture regulation in Tasmania. Assessment of trigger values against proposed sediment and water quality analytes are summarised below. Trigger levels comparisons for sediment For benthic infauna there is considerable subjectivity in the application of proposed risk categories.

For example, the level 1 risk category (i.e. significant change over time at one or more sites) was not

straightforward to apply. At some sites there was an increase in abundance between 2013 and 2017

(e.g. sites B1, B4). However, at these same sites species diversity also increased over the same period.

While changes such as this have occurred between 2013 and 2017 these patterns are not considered

evidence of organic enrichment and were not assessed as level 1 (low risk).

Although guideline values are not specifically defined included for introduced species, the increase in

Varicorbula gibba abundance at some sites (i.e. B4, B10, B13) was notable, with the presence of this

species considered evidence of organic enrichment in muddy habitats. The increase in abundance of

introduced species at these sites was considered a level 1 (low) risk. It should be noted that infauna

trigger level comparisons were somewhat limited due to there being only two datasets involved.

Given the uncertainty surrounding application of trigger values for benthic infauna, it is

recommended that these values are reviewed for future assessments.

Sediment chemistry parameters were generally very similar across survey years. There were

occasional instances where a parameter changed between sampling times which could be interpreted

as a level 1 risk. For example, variation in the magnitude of redox potential was recorded at some

sites between sampling events. Importantly, such variation was not consistent with broad scale

organic enrichment effects and is likely due to the inherent vagaries of redox measurement. As

outlined in the BEMP 2012 review, it would be worthwhile to include the direction, scale of change

and reference to deterioration in sediment condition to allow more meaningful interpretation of

sediment chemistry against trigger values.

Trigger levels comparisons for water quality For water quality a range of trigger values were assessed, incorporating nutrients (ammonia), chlorophyll a, phytoplankton bloom frequency, and dissolved oxygen. The classification of trigger values depended on the analyte concerned and in some cases involved a complex range of criteria. There were a number of examples of level 1 (low risk) ammonia trigger values being reached in the reporting period, but for the majority of sites there was no evidence of an increasing frequency of exceedances over the duration of the monitoring program. Exceptions to this general pattern were evident at sites 8 and 9 in the D’Entrecasteaux Channel and site 10 in the Huon. At these sites there was a tendency for an increased frequency of exceedances based on summer mean values. Level 2 (moderate risk) levels were reached for the Huon MFDP based on average summer mean values in


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2014/15 (summer mean up 50% relative to baseline) and the site level mean for site 10 (mean up 200% relative to baseline). Summer mean ammonia values measured in 2014/15 at site 10 were the highest recorded since the inception of the BEMP program. Although recent years have seen relatively high summer ammonia levels at site 10, it should be noted that similarly high values have been recorded previously (e.g. 2009/10; level 2 moderate risk level). For chlorophyll a analyses there were occasional level 1 (low risk) levels reached based on individual sites across the reporting period. When average values across each MFDP were considered for the 2012/13-2016/17 reporting period there were four level 2 (moderate risk, i.e. summer mean + 100% or annual mean +50%) and three level 1 (low risk, i.e. summer mean +50%) exceedances evident. When all survey years were considered, there was no indication of an increase in the frequency of trigger levels being reached. Exceedances of proposed trigger levels appear linked to seasonal phytoplankton blooms which vary considerably in their timing, frequency and intensity. The proposed chlorophyll a trigger values were considered very complex to apply and interpret, since they incorporate specific sites as well as MFDP areas. As part of the review of trigger levels planned by the EPA, consideration of the approach to analysis of chlorophyll a is recommended. For dissolved oxygen (absolute and % saturation), there were no instances of trigger levels being reached for the D’Entrecasteaux Channel region across the reporting period. For the Huon sites level 1 (low risk; any 2 channel observations ≤ 6 ppm; any 2 bay observations ≤ 5 ppm) was reached in most years. Overall, there was no evidence of an increase in trigger level exceedances based on oxygen concentration or saturation during the reporting period.


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Contents

1. Operational Summary ................................................................................................................................................... 10

2. Introduction .................................................................................................................................................................. 11

3. Methods ........................................................................................................................................................................ 14

3.1 Sediment ..................................................................................................................................................................... 15 3.1.1 Benthic infauna ................................................................................................................................................. 15 3.1.2 Visual assessment, redox potential and sulphide concentration ...................................................................... 15 3.1.3 Stable Isotope and particle size analysis ........................................................................................................... 15

3.2 Water Quality .............................................................................................................................................................. 16

3.2.1 Physico-chemical parameters ........................................................................................................................... 16 3.2.2 Nutrients ........................................................................................................................................................... 17 3.2.3 Phytoplankton ................................................................................................................................................... 17

3.3 Quality Assurance/Quality Control ............................................................................................................................. 18

4. Results and Interpretation ............................................................................................................................................ 19 4.1 Sediment ..................................................................................................................................................................... 19

4.1.1 Benthic infauna ................................................................................................................................................. 19 4.1.2 Visual assessment ............................................................................................................................................. 26 4.1.3 Redox Potential ................................................................................................................................................. 30 4.1.4 Sulphide concentration ..................................................................................................................................... 30 4.1.5 Particle size analysis (i.e. 2009 v 2013) ............................................................................................................. 31 4.1.6 Stable isotope analysis (i.e. 2009 v 2013) ......................................................................................................... 32

4.2 Comparison with proposed Trigger Values - Sediments ............................................................................................. 34 4.3 Water Quality .............................................................................................................................................................. 36

4.3.1 Physico-chemical parameters ........................................................................................................................... 36 4.3.2 Nutrients ........................................................................................................................................................... 40 4.3.3 Phytoplankton ................................................................................................................................................... 48

4.4 Comparison with proposed Trigger Values – Water Quality ...................................................................................... 54

4.4.1 Nutrients - ammonia ......................................................................................................................................... 55 4.4.2 Chlorophyll/algal blooms .................................................................................................................................. 58 4.4.5 Dissolved oxygen (saturation) ........................................................................................................................... 64

4.5. Quality Assurance ...................................................................................................................................................... 67 5. References .................................................................................................................................................................... 69

List of Figures Figure 1 Map of sediment sites (B1-B15) and water monitoring sites (M1-M15) ............................................................... 13 Figure 2 Number of families per site in 2009 and 2013. ...................................................................................................... 20 Figure 3 Number of animals per site in 2009 and 2013. ...................................................................................................... 20 Figure 4 K-dominance plot for based on pooled 2009 survey (family level data) .............................................................. 23 Figure 5 K-dominance plot for based on pooled 2013 survey (family level data) ............................................................... 23 Figure 6 Results of MDS analysis using benthic faunal data collected from replicate grabs at each site in 2013. Ellipses

indicate community similarity (%), based on cluster analysis. Group 1 = Recherche Bay control site; group 2 = northern and mid-channel sites; group 3 = East Lippies; group 4 = Muddy D’Entrecasteaux Channel and Huon sites..................................................................................................................................................................................... 24


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Figure 7 Results of MDS analysis using benthic faunal data collected from replicate grabs at each site in 2009. Ellipses indicate community similarity (%), based on cluster analysis. Group 1 = Recherche Bay control site; group 2 = northern and mid-channel sites; group 3 = East Lippies; group 4 = Muddy D’Entrecasteaux Channel and Huon sites..................................................................................................................................................................................... 25

Figure 8 Results of MDS analysis using benthic faunal data collected from pooled grabs at each site in 2009 and 2013. Ellipses indicate community similarity (%), based on cluster analysis. ...................................................................... 25

Figure 9 Mean corrected redox potential observations, n = 3 (± standard error). .............................................................. 30 Figure 10 Corrected sulphide concentration results as an average at each of the 15 sites from 2009-2016, n = 3 (±

standard error). .......................................................................................................................................................... 31 Figure 11 Mean particle size content (%) of gravel (> 2 mm), sand (0.125-2 mm) and Mud/Silt (< 0.63 mm) for 2009 and

2013. .......................................................................................................................................................................... 32 Figure 12 C/N ratio (± standard error) at each site in 2009 and 2013. ................................................................................ 33 Figure 13 Δ13C versus Δ15N values for samples collected in 2009 and 2013. .................................................................... 33 Figure 14 Spatial and temporal variation in temperature (°C) at three depths (Surface, 5m, Bottom). ............................. 37 Figure 15 Spatial and temporal variation in Dissolved Oxygen (mg/L) at three depths (Surface, 5m, Bottom).................. 38 Figure 16 Spatial and temporal variation in salinity (ppt) at three depths (Surface, 5m, Bottom). .................................... 39 Figure 17 Spatial and temporal variation in ammonia concentration (mg-N/L) at two depths (Surface, Bottom). ............ 42 Figure 18 Spatial and temporal variation in nitrate concentration (mg-N/L) at two depths (Surface, Bottom). ................ 43 Figure 19 Spatial and temporal variation in phosphate concentration (mg-P/L) at two depths (Surface, Bottom). .......... 44 Figure 20 Spatial and temporal variation in silicate concentration (mg/L) at two depths (Surface, Bottom). .................... 45 Figure 21 Spatial and temporal variation in total nitrogen concentration (mg-N/L) at two depths (Surface, Bottom). ..... 46 Figure 22 Spatial and temporal variation in total phosphorous concentration (mg-P/L) at two depths (Surface, Bottom).

.................................................................................................................................................................................... 47 Figure 23 Spatial and temporal variation in chlorophyll a concentration (mg/m3) from integrated samples (12 m). ........ 49 Figure 24 Abundance of phytoplankton groups between March 2009 and February 2017. Data represent mean cell

counts/mL across all sites for each sampling event. .................................................................................................. 51 Figure 25 Relative abundance of harmful and non-harmful algal species between March 2009 and February 2017. Data

represent mean cell counts/mL across all sites for each sampling event .................................................................. 52 Figure 26 Abundance of phytoplankton groups across sampling years for the D’Entrecasteaux, Huon and control sites

(Note: control = 1 site; D’Entrecasteaux = 9 sites; Huon = 5 sites). ........................................................................... 53 Figure 27 Relative abundance of diatom genera (Bacilliarophyta) across sampling years. ................................................. 53 Figure 28 Summer and annual average ammonium concentrations measured during the BEMP program against the

proposed baseline (black line) and 3 trigger levels (dashed horizontal lines +25%, +50%, +100%) in the D’Entrecasteaux Channel (upper panel) and Huon Estuary (lower panel). ................................................................ 56

Figure 29 Average ammonia concentrations over summer for individual sites showing the proposed baseline (black line) and 3 trigger levels (dashed horizontal lines +25%, +50%, +100%) in the D’Entrecasteaux Channel (upper panel) and Huon Estuary (lower panel). ................................................................................................................................ 57

Figure 30 Mean summer and annual average chlorophyll a concentrations at each site measured during the BEMP program. ..................................................................................................................................................................... 60

Figure 31 Annual and summer average chlorophyll a concentrations measured during the BEMP compared to proposed baseline and trigger levels in the D’Entrecasteaux Channel (top panel) and Huon Estuary (bottom panel). Baseline annual values represented by blue line; dashed blue lines represent +50 (level 2 moderate risk) and +100% (level 3 high risk) relative to baseline values. Baseline summer values represented by red line; dashed red lines represent +50 (level 1 low risk), +100% (level 2 moderate risk) and +200% (level 3 high risk) relative to baseline values. ...... 61

Figure 32 Bottom water dissolved oxygen concentrations (mg/L) measured during the BEMP program against the proposed baselines for bay and channel sites in the D’Entrecasteaux Channel (upper panel) and Huon (lower panel). ........................................................................................................................................................................ 63

Figure 33 Bottom water dissolved oxygen concentration saturation (%) measured during the BEMP program against the proposed baselines for bay and channel sites in the D’Entrecasteaux Channel (upper panel) and Huon (lower panel). Blue dashed line = 20th percentile - Bay; red dashed line = 20th percentile - Channel. .................................. 65


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List of Tables Table 1 Survey frequency, sample sites, sample numbers and method for each analyte. ................................................. 12 Table 2 Site descriptions for water quality and sediment monitoring. ............................................................................... 14 Table 3 Summary of water quality laboratory analysis and methods for determination of nutrients and

chlorophyll/microalgae. ............................................................................................................................................. 17 Table 4 Diversity (family level) of benthic invertebrates recorded during 2009 and 2013 surveys. ................................... 21 Table 5 Abundance of benthic invertebrates recorded during 2009 and 2013 surveys. Other category = Platyhelminthes,

sipunculids, cnidarians, nematodes and nemerteans. ............................................................................................... 21 Table 6 Introduced benthic invertebrates recorded from the 2009 and 2013 surveys ....................................................... 22 Table 7 Sediment core descriptions from March 2016 ....................................................................................................... 27 Table 8 Recommended trigger levels for benthic monitoring program parameters with 3 levels of trigger values.

Modified from Thompson et al. 2008 ........................................................................................................................ 35 Table 9 Standard or baseline values proposed for relevant water quality parameters – adapted from Thompson et al.

(2008). ........................................................................................................................................................................ 54 Table 10 – Summary of trigger level comparisons for ammonia. N = trigger level not reached; yellow = level 1, green =

level 2, orange = level 3. Depth: S = surface; B = bottom. Note that for individual sites, the level presented is the maximum risk level observed across all sites for each MFDP. ................................................................................... 58

Table 11 Maximum yearly exceedance level for annual chlorophyll for individual sites in the D’Entrecasteaux and Huon MFDP. N = trigger level not reached; yellow = level 1 (annual mean +100%), green = level 2 (annual mean +200%), orange = level 3 (annual mean +400%). Baseline values for sites were sourced from Thomspon et al 2008. .......... 59

Table 12 – Summary of trigger level comparisons for chlorophyll a based on average summer and annual values for the D’Entrecasteaux Channel and Huon MFDP’s. N = trigger level not reached; yellow = level 1 (average summer mean +50%), green = level 2 (Average summer mean +100%; or Average annual mean +50%), orange = level 3 (Average summer mean +200%; or average annual mean +100%). Baseline average values were sourced from Thompson et al 2008. ....................................................................................................................................................................... 59

Table 13 Calculation of summary statistics and bloom frequency from integrated chlorophyll-a samples collected during the BEMP period, March 2009 – Feb 2017 in the D’Entrecasteaux Channel and Huon MFDP areas. Examples where trigger values are reached during the reporting period are highlighted in green, past exceedances are highlighted in yellow. .................................................................................................................................................................... 62

Table 14 Total number of observations and number of observations below the proposed baseline values of absolute concentrations of bottom water dissolved oxygen (mg/L) since 2009. ..................................................................... 64

Table 15 20th percentile of bottom water dissolved oxygen (% saturation) from 1st year of observations (i.e. 2009/10) and number of observations below the proposed baseline in each year. ................................................................. 66

Table 16–QA duplicate sample results where differences were less than or greater than the minimum reporting limit. Note MRL for Nitrate, Silicate and Chlorophyll a remained unchanged over surveys 51-121. The QA/QC samples incorporated 71 sampling events from May 2012-Februaryu 2017 .......................................................................... 67

Table 17– QA Trip and Field blank sample results where differences were greater than the MRL. Not MRL for nitrate and silicate remained unchanged over the survey period. The QA/QC samples incorporated 71 sampling events from May 2012-February 2017. .......................................................................................................................................... 68

List of Appendices Appendix 1 (a) Sediment core descriptions 2012 ................................................................................................................ 71 Appendix 2 Stable isotope raw data .................................................................................................................................... 87 Appendix 3 (a) Temporal variation in temperature (°C) at three depths (Surface, 5m, Bottom) for each site, March 2009-

February 2017. ........................................................................................................................................................... 88 Appendix 4 (a) Temporal variation in ammonia concentration (mg-N/L) at two depths (Surface, Bottom) for each site,

March 2009-February 2017. ....................................................................................................................................... 91 Appendix 5 Temporal variation in chlorophyll a concentration (mg/m3) for each site, March 2009-February 2017. ........ 97 Appendix 6 (a) Abundance of phytoplankton between March 2009 and February 2017 at each site: Sites 1-3. ............... 98 Appendix 7 Conversion of ammonia baseline levels from CSIRO to AST data. Details below were provided by IMAS. ... 103 Appendix 8 QA/QC analyses – duplicate sample comparisons. Error bars indicate ± MRL values aligned with the sample

value. MRL values are included at the bottom of each figure. Note that surveys 51-80 = May 2012-April 2014; surveys 81-121 = May 2014-February 2017. ............................................................................................................ 105

Appendix 9 QA/QC analyses – field and trip blank comparisons. Error bars indicate ± MRL values aligned with the trip blank value. MRL values are included at the bottom of each figure. Note that surveys 51-80 = May 2012-April 2014; surveys 81-121 = May 2014-February 2017. .................................................................................................. 109


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1. Operational Summary Organisation Conducting Environmental Assessment: Aquenal Pty Ltd ABN 86 081 689 910 244 Summerleas Rd Kingston Tasmania 7050 Phone 03 6229 2334 Fax 6229 2335 e-mail: [email protected] Details of Equipment Used for Sampling:

• Yeo-Kal YK-611 water quality analyser (DO concentration and saturation, temperature, salinity)

• Niskin bottle (bottom nutrient samples) • Pole sampler (surface nutrient samples) • 14 m length of flexible clear plastic tubing (phytoplankton) • Van Veen grab (benthic infauna) • Craib corer (redox, stable isotopes, particle size and sulphide samples) • WTW pH 320/set-1 meter with Mettler Toledo P14805-DXK-S8/225 combination

redox probe (redox analysis) • WTW pH 320/set-1 meter with uniPROBE Sulphide Ion selective Electrode Connector

probe (sulphide analysis) • Garmin/Omnistar™ GPS system (site location)

Vessel: Katelysia - 6.7 m aluminium twin hull Aquenal survey vessel

Laboratories:

Laboratory Address Analytes

Aquenal Pty Ltd 244 Summerleas Rd Kingston, TAS 7050

Sediments: Benthic infauna, redox, sulphide, particle size Water: DO, salinity, temperature, DO saturation

Analytical Services Tasmania

New Town Laboratory 18 St Johns Avenue, New Town, TAS 7008

Water: TN, TP, Phytoplankton cell counts, chlorophyll a, and abundance/diversity

CSIRO Castray Esplanade Hobart TAS 7000 GPO Box 1538 Hobart TAS 7001

Phytoplankton HPLC (samples archived only)


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2. Introduction The Broadscale Environmental Monitoring Program (BEMP) was developed as a requirement in accordance with the Tasmanian Marine Farm Planning Act 1995. The sampling specifications for this project are included in Schedule 3BEMP to marine farming licences for finfish growing operations located within the D’Entrecasteaux Channel Marine Farm Development Plan (MFDP) and Huon/Port Esperance MFDP 1 areas. Schedule 3BEMP states that monitoring must be undertaken by a consultant acting on behalf of all licensed finfish marine farming lease holders within these areas. Aquenal was engaged as the consultant to perform this programme of work. The BEMP program is aimed at assessing water and sediment quality and benthic infauna health at a broad scale at a number of sites in the D’Entrecasteaux Channel and Huon Estuary. The monitoring program design was largely structured around recommendations of previous studies undertaken in the region (e.g. Thompson et al. 2008, Volkman et al. 2009). The monitoring program has water quality and sediment monitoring aspects, each containing a range of analytes/parameters (Table 1). A total of 15 sites are included in the monitoring program; sites 1-9 in D’Entrecasteaux Channel, 10-14 in the Huon River/Port Esperance and control site 15 in Recherche Bay (see Figure 1). The precise location of water (M1-M15) and sediment (B1-B15) sites are slightly different to align with control site location used in previous monitoring studies. Note that analysis of benthic infauna, stable isotopes and particle size is undertaken every 4 years. In the intervening years, these samples are collected, preserved and retained. Assessment of the samples retained from the intervening years may be required where sediment geo-chemistry parameters (e.g. redox, sulphide) and/or the 4-yearly benthic faunal parameters are triggered. BEMP annual reporting was deferred while the Institute of Marine and Antarctic Studies (IMAS) conducted a detailed data review for the 2009-2012 period, which was reported in 2013 (Ross and Macleod 2013). The IMAS BEMP review covered the period March 2009-March 2012. This current report includes an assessment of water quality and sediment sampling events beginning in March 2012 and ending in February 2017. This equated to 5 BEMP reporting years including 2012/13, 2013/14, 2014/15, 2015/16 and 2016/17. The BEMP reporting period is based upon rolling 12 month periods beginning in March and ending in February the following year. This timing reflects the March starting point of the BEMP program, but it also allows meaningful interpretation of proposed trigger levels that incorporate seasonal aspects (e.g. comparison of summer means). Note that while this report covers the 5 BEMP reporting years, the earlier 2009-2012 data was also included to provide context to time series data. Reporting aspects are consistent with requirements outlined in Schedule 3BEMP.

1The BEMP sampling program includes a single site in the Port Esperance MFDP (Dover). For the purpose of all analyses, this site was included with the Huon MFDP sites. Unless otherwise stated, analysis involving Huon MFDP sites included the Port Esperance site (site 12).


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Table 1 Survey frequency, sample sites, sample numbers and method for each analyte.

Component Analyte/Parameter Frequency

Total number of sites for each sampling event

Total number samples per site for each sampling event

Method

Sed

ime

nt

Biota

• Infauna (baseline collection+ ID/ongoing collection only with infaunal re-evaluation every 4 years)

Annually 15 x 3 (seabed)

Benthic grab

Chemistry

• Redox potential • Stable isotopes

analysis (frequency of sample processing consistent with infauna, above)

• Particle size • Sulphide concentration

Annually 15 x 3 (seabed)

Benthic corer

Wat

er

Qu

alit

y

Nutrients

• Ammonia (total ammoniacal Nitrogen) • Nitrate • Phosphate • Silicon • TN • TP

Monthly May-Jan,

Fortnightly Feb, March, April

15

x 2 (surface/ 1m above seabed)

Pole sampler/ Niskin bottle

Dissolved Oxygen

• DO • Temperature • Salinity • DO saturation

Monthly May-Jan,


15

x 3 (Surface, 5m, 1m above seabed)

DO/Temp/ Salinity Meter.

Phytoplankton

• HPLC • Cell counts • Chlorophyll a • Abundance/diversity

Monthly May-Jan,


15

x 1 (12m depth integrated)

Integrated sampler


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Figure 1 Map of sediment sites (B1-B15) and water monitoring sites (M1-M15)


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3. Methods

Before commencing each sampling event the vessel GPS system was calibrated against a State Permanent Mark (SPM). The GPS was used to locate the sites described in Table 2. During each sampling event site positions were recorded by marking them on the GPS. Table 2 lists the coordinates for all sites in the monitoring program. Sites M1, M3, M5, M6 M9, M10, M14 and M13 were designated mid-channel sites and M2, M4, M7, M8, M11, M12 were designated as bay sites. Table 2 Site descriptions for water quality and sediment monitoring.

Site Name Type Location MFDP area Classification Easting Northing

M1 Water Northern Boundary Boundary Channel 527684.3 5232077.5

M2 Water Northwest Bay D'Entrecasteaux Bay 523534.9 5233037.0

M3 Water Upper Mid Channel D'Entrecasteaux Channel 523752.2 5225262.6

M4 Water Barnes Bay D'Entrecasteaux Bay 526513.4 5224119.7

M5 Water Green Island D'Entrecasteaux Channel 524124.6 5215636.6

M6 Water Central Mid Channel D'Entrecasteaux Channel 515244.9 5204098.0

M7 Water Little Taylors Bay D'Entrecasteaux Bay 516856.5 5200018.5

M8 Water Great Taylors Bay D'Entrecasteaux Bay 512706.9 5191231.9

M9 Water Southern Boundary Boundary Channel 505506.1 5194295.7

M10 Water Lower Huon Huon Channel 506737.0 5210741.8

M11 Water Cygnet Huon Bay 507312.3 5217304.4

M12 Water Dover Port Esperance Bay 502675.3 5202537.7

M13 Water Upper Huon Huon Channel 498550.0 5222185.0

M14 Water Mid Huon Huon Channel 500649.9 5216586.4

M15 Water Recherche Control Control (Bay) 492064.0 5178637.0

B1 Sediment Northern Boundary Boundary 527388.0 5232358.0

B2 Sediment Northwest Bay D'Entrecasteaux 524236.0 5233512.1

B3 Sediment Sheppards Point D'Entrecasteaux 524089.1 5227962.0

B4 Sediment Roberts Point D'Entrecasteaux 525224.1 5224328.0

B5 Sediment Soldiers Point D'Entrecasteaux 522337.1 5219689.9

B6 Sediment Green Island D'Entrecasteaux 524124.6 5215636.6

B7 Sediment Zuidpool D'Entrecasteaux 512422.5 5202009.5

B7 (revised)* Sediment Zuidpool D'Entrecasteaux 511188.0 5202954.0

B8 Sediment Great Taylors Bay D'Entrecasteaux 512028.0 5194349.6

B9 Sediment Lippies Point Boundary 504494.8 5195744.8

B10 Sediment Garden Island Huon 507993.2 5210570.8

B11 Sediment Deep Bay Huon 507095.0 5213795.3

B12 Sediment Dover Port Esperance 502357.1 5202638.7

B13 Sediment Pillings Bay Huon 498167.8 5220383.2

B14 Sediment Brabazon Point Huon 500172.0 5217257.8

B15 Sediment Recherche Bay Control 492064.0 5178637.0

*Note that location of site B7 required adjustment in 2016, due to its close proximity to the amended Zuidpool (MF141) lease. The new site B7 was located approximately 1.5 km from the original location, in the same depth range as the original site.


15

3.1 Sediment

3.1.1 Benthic infauna Infaunal samples were collected by triplicate Van Veen grabs at each site in March/April 2009 and 2013. The grab samples were washed through an aluminium funnel into polypropylene bags with a mesh size of 0.8 mm. The bagged samples were labelled and placed into a 20 L drum of 10% buffered formalin for a minimum of three days. In the laboratory, collected material was washed through a 1 mm sieve and the retained material was sorted under a dissecting microscope to separate animals from other material. All specimens were placed in labelled vials and preserved in 70% alcohol for longer term storage. Identification and analysis of benthic infauna was undertaken every 4 years, with samples in the intervening years archived, as per the 3BEMP schedule requirements. Macrofaunal data from triplicate grabs were analysed using multidimensional scaling (MDS) in the PRIMER software package (Clarke & Gorley 2001). This analysis produces the best graphical depiction of faunal similarities between samples. For MDS analyses, the data matrix showing total abundance of species in each sample was fourth root-transformed and then converted to a symmetric matrix of biotic similarity between pairs of samples using the Bray-Curtis similarity index. These procedures follow the recommendations of Faith et al. (1987) and Clarke (1993) for data matrices with numerous zero records. The usefulness of the two dimensional MDS display of relationships between samples is indicated by the stress statistic, which, if <0.1 indicates that the depiction of relationships is good, and if >0.2 that the depiction is poor (Clarke, 1993). Triplicate grabs were also aggregated for each site and analysed for faunal dominance with K-Dominance Curves using the PRIMER software package (Clarke & Gorley 2001). 3.1.2 Visual assessment, redox potential and sulphide concentration Triplicate sediment cores were collected at each site using a Perspex corer with a 50 mm diameter. A visual assessment of each core was conducted at the Aquenal laboratory and samples removed for determining sulphide concentration, particle size analysis and stable isotope analysis. The visual assessment included measurement of core length, sediment colour (using a Munsell soil chart), assessment of plant/animal life and assessment for gas vesicles and smell (indicating presence/absence of hydrogen sulphide). Redox potential was measured in each core on return to the laboratory at the end of each field day. Redox potential was measured at a depth of 3 cm from the top of the cores, using a WTW pH 320/set-1 meter with Mettler Toledo P14805-DXK-S8/225 combination redox probe. The probe was calibrated prior to analysis and allowed to stabilise before taking measurements using the methods described in Macleod and Forbes (2004). The sulphide probe was conditioned and calibrated according to Macleod and Forbes (2004) before analysis of sediment from the cores. A sediment sub-sample of 2 ml was extracted from a port in the side of each core tube using a 5 ml syringe, and placed in a glass vial. Added to each jar was 2 ml SAOB (refer to Macleod et al. 2004) and sulphide concentration measured (mV) by placing the probe into the jar, and slowly stirring the sediment/buffer mix until the reading stabilised. The mV readings were converted to sulphide concentration using the calibration curve prepared prior to the analysis being undertaken. 3.1.3 Stable Isotope and particle size analysis The top 3 cm of each core was frozen for stable isotope analysis and the top 10 cm frozen for particle size analysis. Stable isotope and particle size analysis were undertaken every four years to align with benthic infauna sampling. In intervening years particle size and stable isotope samples were frozen


16

and archived. Stable Isotope analysis was conducted by Environmental Isotopes Pty Ltd. Particle size analysis was undertaken in the Aquenal laboratory sing a wet sieve method.

3.2 Water Quality Table 3 summarises the laboratories and analytical techniques for water quality parameters included in the BEMP program.

3.2.1 Physico-chemical parameters Temperature, dissolved oxygen (DO; mg/L and % saturation) and salinity was measured using a Yeo-Kal YK-611 water quality analyser. Measurements were taken at the surface (0.1 m), 5 m and at 1 m above the seabed in accordance with the instrument operation manual supplied by the manufacturer. The water quality analyser was checked or calibrated in accordance with the manufacturer’s requirements prior to each day of sampling. Water quality parameters were stored on the internal memory for each sample and downloaded each day upon return to the laboratory. Key water quality parameters were also scribed in the field. 3.2.2 Nutrients Analytical Services Tasmania (AST) conducted all testing for Total Nitrogen (TN) and Total Phosphorous (TP). CSIRO Marine Laboratories (Hobart) analysed samples for ammonium, nitrate, phosphate and silica concentrations from 2009 until April 2012, while AST analysed these dissolved nutrients from May 2012 onwards. It is known from an interlaboratory comparisons (Eriksen, 2009) that there is some discrepancy in the measurement of ammonia concentration between CSIRO and AST laboratories. Fortunately, AST were contracted to measure total N and total P for the entire BEMP monitoring period and, when measuring total N, also measured ammonia (and nitrate) concentration. This AST data was provided for the current analyses, allowing a consistent approach to analysis for these particular analytes.

Sample Collection for Nutrient Determination

A Niskin bottle was used for collecting bottom water (i.e. 1 m above the seabed), while a pole sampler was used to collect surface samples. Sample containers were filled from the Niskin bottle/pole sampler and stored on ice until return to the laboratory. With the exception of silicate samples which where refrigerated, nutrient samples were frozen before delivery to the AST laboratories. AST nutrient samples were filtered at the time of collection using disposable hermetically sealed syringes and 0.45 μm PES filters.


17

Table 3 Summary of water quality laboratory analysis and methods for determination of nutrients and chlorophyll/microalgae.

Laboratory Analytes Methods Analysis period

Analytical Services Tasmania (AST)

Total N, Total P, ammonia, nitrate

Phytoplankton cell counts, macroalgal cell abundance/diversity

chlorophyll a

Total nutrients by Kjeldahl Digest and Flow Injection Analysis.

Micro algal cell counts and abundance/diversity by microscopic observation.

Spectrophotometry

March 2009-February 2017

Phosphate, silicate Dissolved nutrients by Flow Injection Analysis

June 2012-February 2017

CSIRO

Phosphate, silicate Dissolved inorganic nutrients were determined using colorimetric methods adapted for Flow Injection Analysis on a 5 channel LACHAT Quik-Chem 8000 auto analyser.

March 2009-May 2012

*Phytoplankton pigment concentrations

HPLC March 2009-February 2012

*Note that HPLC samples have been archived but not analysed since February 2012. Detailed phytoplankton data is provided from AST species counts and chlorophyll a analysis.

3.2.3 Phytoplankton Depth integrated samples were collected at each sample site using a 14 m length of flexible clear plastic tubing marked with 1 m graduations. The tube was weighted at the bottom end and lowered through the water column at approximately 1 m/sec to reach a depth of 12 m or within 2 m of the seabed. The tube was then sealed using a bung at the surface to trap the water. The tube was lowered into the water to be thoroughly rinsed before sampling at each site. Once onboard the boat, the sample contents of the tube were poured into a large bucket and gently mixed to achieve homogeneity. Samples were then transferred into a storage container and maintained on ice prior to delivered to the Aquenal laboratory. At the Aquenal laboratory, samples destined for chlorophyll a analysis at the AST laboratories were filtered using a vacuum pump and Millipore filtering units with a Whatman GF/F filter. Filters were frozen before delivery to the AST laboratories. Samples destined for HPLC analysis were filtered using the same apparatus with an Advantec GF75 filter. HPLC samples were transferred to cryovials and stored immediately in liquid nitrogen until delivery to CSIRO. AST conducted analysis for macroalgal cell count, diversity/abundance and chlorophyll a concentration. Sample for HPLC for pigment analyses were archived at the CSIRO laboratories.


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3.3 Quality Assurance/Quality Control

For each sampling event, quality assurance/quality control (QA/QC) samples were collected. There were two main aspects to the QA/QC sampling:

1. Duplicate samples

For each sampling occasion a sample duplicate and filtered sample was taken from one randomly selected sample site (surface and bottom). All nutrients were analysed in the duplicate sample. Duplicate chlorophyll a samples were also collected from a single integrated depth sample on each sampling occasion.

2. Trip/Field blanks

Field and trip blanks were supplied by AST and included for each sampling event. The field blank was taken on the survey before being transferred and filtered on board the vessel. The trip blank was also taken on the survey but remained unopened. Trip and field blanks were stored and transported in the same manner as the site samples. All nutrients were analysed for the field and trip blank samples.


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4. Results and Interpretation

4.1 Sediment 4.1.1 Benthic infauna A total of 107 benthic infaunal families were recorded from the 45 grab samples collected during the 2013 survey, compared with 104 families recorded in 2009 (Figure 2; Table 4). At the family taxonomic level, diversity at each particular site was remarkably similar between the two surveys (Figure 2; Table 4). Overall abundance was higher in 2013, with 6854 individuals recorded across the 45 samples, compared to 4222 individuals in 2009. Faunal abundance was higher at the majority of sites, however in 2013 abundance was particularly high at sites B1, B4, B5, B10 and B15 (Figure 3, Table 5). Faunal communities were dominated by polychaetes in both surveys, accounting for 41.8% of individuals and 28.9 % of families identified. Crustaceans were also a prominent component of faunal communities, accounting for 35.9% of individuals and 37.4 % of families. Molluscs were also an important component of the fauna in terms of abundance (16.3% of individuals) and diversity (22.2% of families). Patterns of diversity were comparable between surveys. However, abundance patterns showed some variation, with relative abundance of molluscs increasing from 11.8% in 2009 to 20.7% in 2013. Although overall crustacean abundance increased slightly between surveys, relative crustacean abundance declined from 40.0% to 31.7% in 2013. Abundance and diversity of echinoderms and other fauna (including platyhelminths, sipunculids, cnidarians, nematodes and nemerteans) was relatively low and comparable between the 2009 and 2013 surveys. Three species of polychaete from the family Capitellidae (Capitellid sp., Notomastus sp., and Mediomastus australiensis) were recorded, however none of these were from the pollution indicating genus Capitella.


20

Figure 2 Number of families per site in 2009 and 2013.

Figure 3 Number of animals per site in 2009 and 2013.

0

10

20

30

40

50

60

70

B1 B2 B3 B4 B5 B6 B7 B8 B9 B10 B11 B12 B13 B14 B15

Nu

mb

er fa

mili

es

per

sit

e

2009

2013

0

200

400

600

800

1000

1200

B1 B2 B3 B4 B5 B6 B7 B8 B9 B10 B11 B12 B13 B14 B15

Ab

un

dan

ce (

po

ole

d a

cro

ss 3

gra

bs)

2009

2013


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Table 4 Diversity (family level) of benthic invertebrates recorded during 2009 and 2013 surveys.

Site

Crustaceans Molluscs Echinoderms Polychaetes Other

2009 2013 2009 2013 2009 2013 2009 2013 2009 2013

B1 23 26 5 10 1 1 17 22 4 2

B2 6 3 3 7 1 1 12 10 1 2

B3 11 11 6 8 1 2 19 19 2 2

B4 13 16 7 12 0 1 15 21 2 3

B5 23 22 7 8 0 1 23 23 6 4

B6 8 11 7 10 2 1 17 18 4 3

B7 3 6 3 6 2 2 9 7 2 4

B8 4 5 3 4 2 2 10 11 2 2

B9 14 16 7 10 1 2 17 14 2 3

B10 4 4 2 4 1 1 7 9 3 3

B11 3 5 4 4 0 1 7 3 4 3

B12 8 5 7 6 2 2 14 14 2 3

B13 2 5 4 3 0 1 7 5 0 3

B14 2 6 2 4 1 1 8 5 3 3

B15 7 7 1 9 0 1 10 11 0 1

Total 42 40 21 26 4 4 31 30 6 7

% 40.4 37.4 20.2 24.3 3.8 3.7 29.8 28.0 5.8 6.5

Table 5 Abundance of benthic invertebrates recorded during 2009 and 2013 surveys. Other category = Platyhelminthes, sipunculids, cnidarians, nematodes and nemerteans.

Site

Crustaceans Molluscs Echinoderms Polychaetes Other

2009 2013 2009 2013 2009 2013 2009 2013 2009 2013

B1 125 314 99 164 4 4 127 481 5 8

B2 35 20 23 93 22 13 133 89 3 21

B3 146 167 31 31 6 3 267 337 12 22

B4 79 88 12 426 0 1 112 451 3 15

B5 147 313 18 39 0 1 457 542 67 26

B6 54 72 15 60 3 1 123 214 26 52

B7 33 54 25 78 7 3 52 91 8 25

B8 41 55 40 45 4 7 37 104 16 22

B9 820 707 23 82 11 19 127 133 7 14

B10 11 35 32 162 5 5 38 70 15 20

B11 10 39 20 59 0 1 40 12 16 13

B12 64 43 102 59 11 10 170 148 10 22

B13 17 37 34 61 0 1 22 19 0 17

B14 8 63 16 24 3 5 16 14 8 32

B15 100 169 8 38 0 2 41 165 0 2

Total 1690 2176 498 1421 76 76 1762 2870 196 311

% 40.0 31.7 11.8 20.7 1.8 1.1 41.7 41.9 4.6 4.5


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Pollution indicator species Representatives from the family Capitellidae, Notomastus sp. and Mediomastus australiensis were recorded in both surveys, with M. australiensis abundance increasing from 330 individuals in 2009 to 790 individuals in 2013. While some capitellids can be indicators of organic enrichment, Notomastus sp. and M. australiensis are not regarded as a pollution indicator species. Introduced species Five introduced species were collected across all samples in 2009 and 2013. The most common and widely distributed of these species were the molluscs Maoricolpus roseus, Theora lubrica and Varicorbula gibba. While the diversity of introduced taxa was comparable between 2009 and 2013, abundance tended to be higher in 2013. Varicorbula gibba abundance, in particular, was considerably higher in the 2013 survey. This was mainly due to increased abundance at sites B4, B10 and B13 (see Table 6). Table 6 Introduced benthic invertebrates recorded from the 2009 and 2013 surveys

Phylum Arthropoda Mollusca Mollusca Mollusca Annelida

Family Caprellidae Turritellidae Semelidae Corbulidae Sabellidae

Species Caprella acanthogaster

Maoricolpus roseus Theora lubrica

Varicorbula gibba Euchone limnicola

Year 2009 2013 2009 2013 2009 2013 2009 2013 2009 2013

B1 0 0 92 139 0 0 0 6 0 0

B2 0 0 0 0 17 48 0 33 5 5

B3 0 0 0 0 22 19 1 5 8 0

B4 1 0 3 38 4 94 0 268 1 0

B5 0 0 5 20 5 6 0 3 11 2

B6 0 0 1 7 4 17 3 23 0 1

B7 0 0 0 0 18 64 0 1 0 1

B8 0 0 0 0 10 35 0 1 2 0

B9 0 0 10 5 0 0 0 1 0 0

B10 0 0 0 0 31 50 0 100 0 1

B11 0 0 0 0 10 42 8 11 0 0

B12 0 0 0 0 67 33 3 4 30 22

B13 0 0 0 0 24 21 0 37 3 0

B14 0 0 0 0 15 17 0 5 1 0

B15 0 0 0 0 0 0 0 0 0 1

Total 1 0 111 209 227 446 15 498 61 33

K-dominance plots are frequently used to monitor the health of benthic infauna populations and were applied to compare levels of family level dominance across the study area and between years (Figure 4, Figure 5). Two features of the plots provide information about dominance: the y-intercept (i.e. a large value indicates there is one family that is highly dominant) and the slope (i.e. a steep slope indicates that a small number of species dominate the community). Sites that are dominated by a small number of taxa are generally considered of lower environmental health than areas characterised by a larger number of less dominant taxa. The K-dominance plots between 2009 and 2013 were very similar, with relatively low levels of dominance by a single family. Overall, the average level of single family dominance across all sites


23

was 25.1% in 2013, compared to 26.8% in 2009. In both survey years, cumulative dominance was highest at site 9. This was attributable to relatively high abundance of amphipod crustaceans from the family Ampeliscidae. This family is not considered to be a nutrient indicator species. Overall, based on the k-dominance patterns there was no evidence of a change in community composition attributable to organic enrichment.

Figure 4 K-dominance plot for based on pooled 2009 survey (family level data)

Figure 5 K-dominance plot for based on pooled 2013 survey (family level data)

1 10 100

Species rank

0

20

40

60

80

100

Cum

ula

tive

Dom

inance%

B1

B2

B3

B4

B5

B6

B7

B8

B9

B10

B11

B12

B13

B14

B15

1 10 100

Species rank

0

20

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B1

B2

B3

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B5

B6

B7

B8

B9

B10

B11

B12

B13

B14

B15


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Multi-dimensional Scaling plots and cluster analysis of 2013 replicate data revealed the presence of four distinct faunal communities, reflecting broad spatial differences and variation in habitat (Figure 6):

Group 1 Recherche Bay control site (B15) Group 2 Northern and mid-channel sites (B1, B3, B4, B5, B6) Group 3 East Lippies (B9) Group 4 Muddy D’Entrecasteaux Channel and Huon sites (B2, B7, B8, B10, B11, B12,

B13, and B14) Similar patterns were evident in 2009 (Figure 7), although in 2009 the northern channel site B1 separated from the remaining channel sites and there was also some replicates (i.e. B10.3 and B14.1) that didn’t clearly fall within the main site groupings at the 40% similarity level. Analysis of pooled replicate data enabled comparison of community patterns between the 2009 and 2013 surveys (Figure 8). Sample sites across both the 2009 and 2013 surveys separated into the four main four broad groupings identified above. Importantly, this analysis showed no clear divergence in community structure between the 2009 and 2013 surveys, with sites showing general alignment between the two survey years (Figure 8).

Figure 6 Results of MDS analysis using benthic faunal data collected from replicate grabs at each site in 2013. Ellipses

indicate community similarity (%), based on cluster analysis. Group 1 = Recherche Bay control site; group 2 = northern

and mid-channel sites; group 3 = East Lippies; group 4 = Muddy D’Entrecasteaux Channel and Huon sites.


25

Figure 7 Results of MDS analysis using benthic faunal data collected from replicate grabs at each site in 2009. Ellipses

indicate community similarity (%), based on cluster analysis. Group 1 = Recherche Bay control site; group 2 = northern

and mid-channel sites; group 3 = East Lippies; group 4 = muddy D’Entrecasteaux Channel and Huon sites.

Figure 8 Results of MDS analysis using benthic faunal data collected from pooled grabs at each site in 2009 and 2013. Ellipses indicate community similarity (%), based on cluster analysis.


26

In summary, for the majority of benthic community properties examined, there was no evidence of a major shift in species composition or organic enrichment, with faunal communities very similar between 2009 and 2013. The only potential indicator of a decline in ecosystem condition was an increase in abundance of the introduced species Varicorbula gibba and Theora lubrica. Since only two sets of faunal data have been examined it is not clear whether this is an increasing trend or part of a natural cycle. Future benthic analyses of 2017 data will enable improved assessment of introduced species patterns. 4.1.2 Visual assessment Results from visual assessment of cores in 2016 are summarised in Table 7. In 2016 survey the dominant colour in the majority of cores was recorded as dark grey on the Munsell soil chart. Only two sites, B11 and B13, had sediment that was very dark grey and black, respectively. At B1 a change in colour was observed throughout the length of the cores, with darker sediment below the surface sediment. All other sites had a consistent colour throughout the entire length of the core. Sediment type was noted to be either fine or very fine sand in all cores. Shell grit or shell fragments were observed at a number of sites, mostly in the northern channel (i.e. B1, B3, B4, B5, B6), but also in the southern channel at B9. Bioturbation and/or animal life was observed in at least two cores at all sites. Evidence of animal life was observed most frequently in the presence of burrows and observations of gastropods, crustaceans and polychaetes. No odour, gas bubbles were detected from any core. The sediment characteristics in the 2016 survey were similar to previous surveys conducted in the reporting period (i.e. 2012, 2013, 2014 and 2015) and there have been no major changes in sediment characteristics since the inception of the monitoring program. The presence of black sediments or streaking, in particular, can be a good indicator of the presence of sulphide in sediments (Birchenough et al. 2012, Ross and Macleod 2013). There was no evidence an increased presence of darker colouration in sediments over the reporting period. See Appendix 1 for visual sediment descriptions for 2012, 2013, 2014 and 2015.


27

Table 7 Sediment core descriptions from March 2016

Core Length (mm) Colour 1 Sediment 1

Depth 1 (mm) Colour 2 Sediment 2

Depth 2 (mm) Plants Animals Gas Smell

B1.1 180 10YR/4/1 Dark grey Very fine sand, sparse shell grit 0-70 mm 180 Nil

Maoricolpus on sediment surface, burrows Nil Nil

B1.2 120 10YR/4/1 Dark grey Very fine sand 30 10YR/5/1 Grey

Fine sand and shell grit, large shell fragments 120 Nil Burrows Nil Nil

B1.3 140 10YR/4/1 Dark grey Very fine sand 20 10YR/5/1 Grey

Fine sand and shell grit, large shell fragments 140 Nil Burrows Nil Nil

B2.1 160 10YR/4/1 Dark grey Very fine sand 160 Nil Burrows Nil Nil



B3.1 110 10YR/4/1 Dark grey Very fine sand with sparse shell grit 110 Nil

Burrows, ghost shrimp at 70 mm Nil Nil

B3.2 150 10YR/4/1 Dark grey Very fine sand with sparse shell grit 150 Nil Burrows Nil Nil


Burrows, ghost shrimp at 50 mm, worm tubes on sediment surface Nil Nil

B4.1 160 10YR/4/1 Dark grey Very fine sand 5 10YR/4/1 Dark grey

Very fine sand with sparse shell grit 160 Nil Burrows Nil Nil






28








Very fine sand with sparse shell grit Nil Burrows Nil Nil


Worm tube and fan worm on sediment surface Nil Nil


B6.3 160 10YR/4/1 Dark grey Very fine sand with sparse shell grit 160 Nil Nil Nil Nil






B8.3 200 10YR/4/1 Dark grey Very fine sand 200 Nil Burrows, ghost shrimp at 80 mm Nil Nil








29




B11.1 140 10YR/3/1 Very dark grey Very fine sand 140 Nil Nil Nil Nil

B11.2 150 10YR/3/1 Very dark grey Very fine sand 150 Nil Burrows Nil Nil

B11.3 150 10YR/3/1 Very dark grey Very fine sand 150 Nil





B13.1 190 10YR/2/1 Black Very fine sand 190 Nil Burrows Nil Nil


B13.3 170 10YR/2/1 Black Very fine sand 170 Nil Nil Nil Nil







B15.1 150

10YR/4/1 Dark grey, faint dark streaks 70 - 150 mm Fine sand 150 Nil Nil Nil Nil

B15.2 160

10YR/4/1 Dark grey, faint dark streaks 90 - 150 mm Fine sand 160 Nil

Burrows, polychaete at 120 mm, gastropod on sediment surface Nil Nil

B15.3 150

10YR/4/1 Dark grey, faint dark streaks 130 - 150 mm Fine sand 150 Nil Burrows Nil Nil


30

4.1.3 Redox Potential Redox potential readings taken at 3 cm depth in the cores from 2009-2016 are shown in Figure 9. Patterns of redox potential appeared relatively consistent for all survey years. Redox values observed in 2016 were within the range of values observed in the previous years, and there was no evidence of a decrease in redox potential for any of the monitoring sites. Organic enrichment is typically indicated by redox values < 0 mV (Macleod and Forbes 2004), and there has been no such evidence through the course of the monitoring program. At most monitoring sites, average redox values have consistently exceeded 100 mV, these levels are indicative of unimpacted sediments (Macleod and Forbes 2004).

Variation in redox potential values reflects the organic content, grain size composition, biological activity, proximity to the open ocean and the associated level of water movement (and therefore agitation) at the sea bed. Sites subject to greater current and/or wave energy (e.g. B1, B3, B4, B5, B6, B9) generally display higher redox levels than those from more sheltered regions (e.g. B10, B11, B12, B13, B14, B15).

Figure 9 Mean corrected redox potential observations, n = 3 (± standard error).

4.1.4 Sulphide concentration Mean corrected sulphide concentration results for the 2009-2016 period are shown in Figure 10. Sulphide levels have remained very low across all sites and survey events, with the majority of readings close to zero or not detectable. While still at low levels, sulphide levels tend to be slightly higher relative to other sites at B10, B13 and B15. Occasional high variability has been evident (e.g. B1 in 2012), but it should be noted that sulphide analysis is susceptible to occasional anomalous readings which is likely to explain such outliers.


31

Overall, readings in 2016 were comparable with previous years. No site has a sulphide concentration exceeding 100 µM, suggesting that there is no evidence of organic enrichment (Macleod and Forbes 2004).

Figure 10 Corrected sulphide concentration results as an average at each of the 15 sites from 2009-2016, n = 3 (± standard error).

4.1.5 Particle size analysis (i.e. 2009 v 2013) To allow comparison between 2009 and 2013, sediment grain sizes were grouped into conventional

sediment groups of gravel (> 2 mm), sand (0.125 – 1 mm) and silt (≤0.063) (Figure 11).

Patterns of particle size distribution were broadly comparable between the two sampling years

considered. Huon River sites B10, B11, B12, B13 and B14 were dominated by a relatively high silt

content, attributable to their sheltered location. Conversely, sites in the D’Entrecasteaux Channel

(i.e. B1, B3, B4, B5, B6, B9) were typified by a higher proportion of sand particle size fractions. Site

B15 (control site) has the highest sand content of all sites in both years.

Sites B1, B5 and B8 showed some evidence of change between 2009 and 2013, with a higher

proportion of sand particle size fractions measured in 2013. It is unclear whether this represented

a real change in sediment condition or is attributable to sampling variation. Of the sites where

changes were apparent, it is notable that sites B1 and B5 were included. These sites are dominated

by screw shells and collection of undisturbed sediment cores at such sites is very challenging.

Variation in particle size distribution would be expected at these sites since loss of a proportion of

fine silt particle size fractions from core samples is unavoidable when high densities of screw shells

are present. Such site specific habitat characteristics may explain why sediment composition may

not be a particularly sensitive response variable for monitoring environmental change, as concluded

in the 2012 BEMP review (Ross and Macleod 2013).


32

Figure 11 Mean particle size content (%) of gravel (> 2 mm), sand (0.125-2 mm) and Mud/Silt (< 0.63 mm) for 2009 and 2013.

4.1.6 Stable isotope analysis (i.e. 2009 v 2013) Average C:N ratios for each site in 2009 and 2013 are summarized in Figure 12. C:N ratios were

comparable between the two sampling events. The average C:N ratio was typically very similar for

all D’Entrecasteaux Channel sites and the control, averaging 11.37 across both sampling years at

these sites. C:N ratios were much more variable in the Huon sites. The highest values were recorded

for the most upstream site (B13; average 28.36), with a gradient of decreasing C:N ratios evident

with increasing distance downstream (i.e. B13> B14> B11). These patterns are most likely related to

the variation in sediment particle size distribution, depth and organic inputs which characterise the

Huon Estuary.

Patterns of 13C and 15N stable isotope values were generally consistent between 2009 and 2013

(Figure 13). Patterns observed in stable isotope analyses were also broadly consistent with previous

stable isotope analyses for the Huon and D’Entrecasteaux Channel regions (Butler et al. 2000;

Thompson et al. 2008). Typical patterns measured in the BEMP and other studies show Huon sites

to be characterized by material of terrestrial origin with relatively low 13C and 15N values. In the

current study, site B13 showed the lowest average 13C and 15N values across both sampling years

(13C = -26.9%; 15N = 3.15%), with these stable isotope values increasing progressively at sites

further downstream. In contrast, D’Entrecasteaux Channel stable isotope values were more

indicative of material with marine origin, typified by higher 13C and 15N values (13C =-22.59%; 15N

= 7.81%; average values across all D’Entrecasteaux Channel sites).

The results showed no evidence of impacts attributable to fish farming in the study area. Data

covering a greater span of sampling years will be important to determine levels of stable isotope

variation for the D’Entrecasteaux Channel and Huon Estuary.

Raw data from stable isotope analysis is included in Appendix 2.


33

Figure 12 C/N ratio (± standard error) at each site in 2009 and 2013.

Figure 13 Δ13C versus Δ15N values for samples collected in 2009 and 2013.


34

4.2 Comparison with proposed Trigger Values - Sediments Proposed baseline trigger levels established by Thompson et al. (2008) provide a framework for

developing management responses based on guideline or trigger values and the extent to which the

parameter exceeds the trigger value. They also take into account the various risks to ecological

structure and function. It is important to note that the proposed trigger levels are not statutory

limits and their purpose was to inform regulatory management of the industry. It is likely these

guideline values will be reviewed by the EPA following recent changes to aquaculture regulation in

Tasmania. Proposed trigger levels relevant to the sediment assessment are summarised in Table 8

below.

For benthic infauna there is considerable subjectivity in the trigger level risk categories. For example,

the level 1 risk category (i.e. significant change over time at one or more sites) was not

straightforward to apply. At some sites there was an increase in abundance between 2013 and 2017

(e.g. sites B1, B4). However, at these same sites species diversity also increased over the same

period. While changes such as this have occurred between 2013 and 2017, these patterns were not

considered evidence of organic enrichment and were not assessed as level 1 (low risk). Similarly,

based on the multivariate patterns between 2009 and 2013, level 2 (moderate risk) was not reached,

with overall patterns of community structure remarkably similar between 2009 and 2013.

Although guideline values are not currently specifically included for introduced species, the increase

in Varicorbula gibba abundance at some sites (i.e. B4, B10, B13) was notable, with the presence of

this species considered evidence of organic enrichment in muddy habitats (Forbes and Macleod

2004). The increase in abundance of introduced species at these sites was considered a level 1 (low)

risk. Future analysis of samples from the BEMP monitoring program will be important in determining

whether this is an increasing trend, or part of natural ‘boom and bust’ cycles that are often

associated with introduced species.

It should be noted that infauna comparisons were somewhat limited due to there being only two

datasets involved. Given the uncertainty surrounding application of trigger values for benthic

infauna, it is recommended that these values are reviewed for future assessments.

The trigger levels for the sediment chemistry parameters propose that significant change in one

indicator at one site over time constitutes a low level risk, whilst change in two or more sites or

indicators represents a level 2 risk. Change in multiple indicators or at more than one site at a time

provides evidence of a level 3 response. There were occasional instances where a parameter

changed between sampling times which could be interpreted as a level 1 risk based on Thompson

et al. 2008. For example, variation in redox values were recorded at some sites between sampling

events. Importantly, such variation was not consistent with organic enrichment effects and is likely

due to the inherent vagaries of redox measurement. As outlined in the BEMP 2012 review, it would

be worthwhile to include the direction, scale of change and reference to deterioration in sediment

condition to allow more meaningful interpretation of sediment chemistry against trigger values

(Ross and Macleod 2013).

As described for benthic infauna, analysis of stable isotopes and particle size were limited by only 2

sampling events being considered.

Based on the sediment chemistry parameters considered (visual assessment, redox, sulphide, particle size, stable isotopes) for the reporting period 2012-13-2016/2017, there were no consistent trends considered evidence of organic enrichment (see Macleod and Forbes 2004).


35

Table 8 Recommended trigger levels for benthic monitoring program parameters with 3 levels of trigger values.

Modified from Thompson et al. 2008

Parameter Standard or Baseline Value Level 1

(Low risk)

Level 2

(Moderate risk)

Level 3

(High risk) Huon Estuary D’Entrecasteaux

Channel

Sediment

biota

(infauna)

TBD TBD Significant change

over time at one

or more sites

Other indicators

TBD

Significant

change in

multivariate

community

structure at one

site

Other indicators

TBD

Significant change

in multivariate

community

structure at two or

more sites

Other indicators

TBD

Sediment

chemistry

ANZECC

guidelines for

metals and

TBD

ANZECC

guidelines for

metals and TBD

Significant change

over time at one

site

Significant

change over

time at 2 sites/

2 indicators

Exceeding

ANZECC low

guidelines

Significant change

over time at > 3

sites/ 2 indicators

Exceeding ANZECC

high guidelines


36

4.3 Water Quality 4.3.1 Physico-chemical parameters

4.3.1.1 Temperature Water temperatures in the study area showed expected seasonal changes (Figure 14). Surface water temperature showed more variability within the Huon estuary (i.e. sites 11, 13, 14), due to inputs from snow melt and rainfall. Bottom water temperature was generally relatively stable to surface waters. Over the 2012/13-2016/17 reporting period the lowest mean seawater temperatures were recorded in winter 2015 (surface 9.9°C, bottom 11.1°C), while the highest mean temperatures were recorded the following 2015/16 summer (surface 18.5°C, bottom 16.7°C). 4.3.1.2 Dissolved oxygen Patterns of dissolved oxygen concentration are summarised in Figure 15. Across all sampling months, levels of dissolved oxygen were highest at the surface and lowest in bottom waters (Figure 15). Seasonal trends were also evident, particularly in bottom waters, with oxygen concentration reaching minimum levels in late summer and autumn (Figure 15). Patterns of dissolved oxygen were very similar for D’Entrecasteaux Channel sites and the control. Huon River sites, in contrast, showed considerable variation. Bottom water dissolved oxygen concentrations tended to decrease with increasing distance upstream, with lowest average bottom water dissolved oxygen measured at site 13. Patterns of dissolved oxygen across the reporting period were generally comparable to earlier sampling years. 4.3.1.3 Salinity Salinity patterns are summarised in Figure 16. Minimum salinity values were lowest in the upper reaches of the Huon River where freshwater inputs influence surface water conditions. Bottom water salinity showed little variation across sites. Over the reporting period there was very little variation in bottom water salinity, with a mean value of 35.1 ppt recorded. Mean surface salinity showed seasonal variation and averaged 32.1 ppt over the reporting period. Detailed physico-chemical data for each site is included in Appendix 3.


37

Figure 14 Spatial and temporal variation in temperature (°C) at three depths (Surface, 5m, Bottom). Upper panel: Mean monthly temperature from March 2009 to February 2017; Mid-panel: Variation in temperature across sampling months; Lower panel: Variation in temperature across sites; Boxplots are defined by minimum, median and maximum values (lines); 20th and 80th percentiles (boxes); and means (crosshairs). MFDP abbreviations: DC = D’Entrecasteaux Channel, PE = Port Esperance. Note: data gaps were due to problems with the field water quality analyser.


38

Figure 15 Spatial and temporal variation in Dissolved Oxygen (mg/L) at three depths (Surface, 5m, Bottom). Upper panel: Mean monthly Dissolved Oxygen from March 2009 to February 2017; Mid-panel: Variation in Dissolved Oxygen across sampling months; (c) Variation in Dissolved Oxygen across sites; Boxplots are defined by minimum, median and maximum values (lines); 20th and 80th percentiles (boxes); and means (crosshairs). MFDP abbreviations: DC = D’Entrecasteaux Channel, PE = Port Esperance. Note: data gaps were due to problems with the field water quality analyser.


39

Figure 16 Spatial and temporal variation in salinity (ppt) at three depths (Surface, 5m, Bottom). Upper panel: Mean monthly salinity from March 2009 to February 2017; Mid-panel: Variation in salinity across sampling months; Lower panel: Variation in salinity across sites; Boxplots are defined by minimum, median and maximum values (lines); 20th and 80th percentiles (boxes); and means (crosshairs). MFDP abbreviations: DC = D’Entrecasteaux Channel, PE = Port Esperance. Note: data gaps were due to problems with the field water quality analyser.


40

4.3.2 Nutrients 4.3.2.1 Ammonia Patterns of ammonia concentrations are depicted in Figure 17. Ammonia concentrations were higher and more variable in bottom waters compared with surface waters. A seasonal pattern was also evident, particularly in bottom waters (Figure 17). Ammonia concentrations tend to increase during later spring/early summer, with relatively high levels maintained through autumn before declining in early winter. Average ammonia concentrations for D’Entrecasteaux Channel sites were lower and less variable compared to Huon River sites. Highest ammonia levels were recorded at site 13, with mean values steadily declining at downstream sites. There was also a general pattern of declining ammonia concentration in a southerly direction for D’Entrecasteaux Channel sites. Patterns of ammonia concentration within the 2012/13-2016/17 reporting period were generally within the range recorded during previous sampling years at most sites, with peaks in bottom water ammonia largely driven by Huon sites (10-14). At some sites there was a trend of higher ammonia concentrations in the latter part of the reporting period (2014/15 onwards). These slightly higher ammonia levels were most evident at sites 8 and 9 in the D’Entrecasteaux Channel and site 10 in the Huon (see Appendix 4). Average ammonia levels recorded during December 2014 were also among the highest mean values recorded since the inception of the monitoring program (mean bottom water ammonia concentration 0.18 mg-N/L), these levels were mainly driven by high ammonia at sites 10-14, although relatively high levels were also recorded at D’Entrecasteaux Channel sites 2, 6 and 9 over the same period (see Appendix 4).

4.3.2.2 Nitrate Nitrate levels showed a very strong and consistent pattern across all sites, consistent with the annual winter intrusion of nutrient rich southern ocean waters (Figure 18). Nitrate concentrations measured during the reporting period were consistent with those previously recorded in the BEMP program (Figure 18). At some sites, nitrate patterns in surface waters also showed evidence of episodic high concentrations (e.g. site 11, site 13, see Appendix 4). While speculative, these high levels occurred at upstream sites in the Huon and Cygnet areas and are likely to be associated with freshwater run-off events. Following a seasonal peak in winter, nitrate levels in surface waters decline rapidly through spring. This pattern is consistent with uptake by phytoplankton during spring. A similar pattern is evident in bottom waters, however, the rate of decline is slower compared to surface waters.

4.3.2.3 Phosphate Phosphate concentrations also showed seasonal patterns (Figure 19), although not to the degree described for nitrate. Higher autumn and winter phosphate levels are likely to be attributable to rainfall runoff and intrusion of nutrient rich Southern Ocean. Phosphate concentrations in bottom water samples were higher than surface waters but showed greatest divergence in spring and summer, presumably due to uptake by phytoplankton. Note that average phosphate levels appear to be lower in the reporting period compared to 2009-2012 (Figure 19). This is not considered to be a change but reflects the switch from CSIRO to AST laboratories that occurred in May 2012. Over the 2012/13-2016/17 reporting period there was no evidence of changes in phosphate levels, with the range of phosphate concentrations comparable between years.


41

4.3.2.4 Silicate Patterns of silicate concentration are distinct from the other nutrients, as the predominant source of silica in the region is the Huon River (Figure 20). This is most evident when Huon River sites are compared, with highest mean levels recorded at site 13 and a gradient of decreasing silica measured with progression downstream (i.e. site 13> site14 > site 11> site10). In contrast, silicate levels measured at D’Entrecasteaux Channel sites and control site 15 were general low and comparable between sites. Across the reporting period surface water silicate showed fluctuations, likely to be attributable to freshwater flow events. Bottom water silicate levels remained low and relatively stable. Average silicate levels appear to be lower in the reporting period compared to 2009-2012. This is not considered to be an environmental change but reflects the switch from CSIRO to AST laboratories that occurred in May 2012. Over the 2012/13-2016/17 reporting period there was no evidence of a change in silicate, with the range of concentrations comparable between years. 4.3.2.5 Total Nitrogen and Total Phosphorous

Total nitrogen and total phosphorous concentrations are shown in Figures 21 and 22. Total nitrogen tended to be higher in winter although occasional peaks occurred in other seasons, presumably following rainfall events. Surface and bottom water nitrogen levels tend to be similar for most months but showed some divergence in spring/summer, likely due to uptake by phytoplankton activity. Overall there was no clear differences between mean or median values between sites. There were no strong total phosphorous patterns evident, with levels fluctuating within and between years (Figure 22). Bottom water total phosphorous tended to be slightly higher than surface waters in most sampling months. Levels of total nitrogen and total phosphorous in the 2012/13-2016/17 reporting period were within the range recorded in previous sampling years.

Detailed nutrient data for each site is included in Appendix 4.


42

Figure 17 Spatial and temporal variation in ammonia concentration (mg-N/L) at two depths (surface, bottom). Upper panel: Mean monthly ammonia concentration from March 2009 to February 2017; Mid-panel: Variation in ammonia concentration across sampling months; Lower panel: Variation in ammonia concentration across sites (surface and bottom data pooled); Boxplots are defined by minimum, median and maximum values (lines); 20th and 80th percentiles (boxes); and means (crosshairs). MFDP abbreviations: DC = D’Entrecasteaux Channel, PE = Port Esperance. Note that AST data was not available for a small number of sampling events early in the program.


43

Figure 18 Spatial and temporal variation in nitrate concentration (mg-N/L) at two depths (surface, bottom). Upper panel: Mean monthly nitrate concentration from March 2009 to February 2017; Mid-panel: Variation in nitrate concentration across sampling months; Lower panel: Variation in nitrate concentration across sites (surface and bottom data pooled); Boxplots are defined by minimum, median and maximum values (lines); 20th and 80th percentiles (boxes); and means (crosshairs). MFDP abbreviations: DC = D’Entrecasteaux Channel, PE = Port Esperance. Note that AST data was not available for a small number of sampling events early in the program.


44

Figure 19 Spatial and temporal variation in phosphate concentration (mg-P/L) at two depths (surface, bottom). Upper panel: Mean monthly phosphate concentration from March 2009 to February 2017; Mid-panel: Variation in phosphate concentration across sampling months; Lower panel: Variation in phosphate concentration across sites (surface and bottom data pooled); Boxplots are defined by minimum, median and maximum values (lines); 20th and 80th percentiles (boxes); and means (crosshairs). MFDP abbreviations: DC = D’Entrecasteaux Channel, PE = Port Esperance.


45

Figure 20 Spatial and temporal variation in silicate concentration (mg/L) at two depths (surface, bottom). Upper panel: Mean monthly silicate concentration from March 2009 to February 2017; Mid-panel: Variation in silicate concentration across sampling months; Lower panel: Variation in silicate concentration across sites (surface and bottom data pooled); Boxplots are defined by minimum, median and maximum values (lines); 20th and 80th percentiles (boxes); and means (crosshairs). MFDP abbreviations: DC = D’Entrecasteaux Channel, PE = Port Esperance.


46

Figure 21 Spatial and temporal variation in total nitrogen concentration (mg-N/L) at two depths (surface, bottom). Upper panel: Mean monthly total nitrogen concentration from March 2009 to February 2017; Mid-panel: Variation in total nitrogen concentration across sampling months; Lower panel: Variation in total nitrogen concentration across sites (surface and bottom data pooled); Boxplots are defined by minimum, median and maximum values (lines); 20th and 80th percentiles (boxes); and means (crosshairs). MFDP abbreviations: DC = D’Entrecasteaux Channel, PE = Port Esperance.


47

Figure 22 Spatial and temporal variation in total phosphorous concentration (mg-P/L) at two depths (surface, bottom). Upper panel: Mean monthly total phosphorous concentration from March 2009 to February 2017; Mid-panel: Variation in total phosphorous concentration across sampling months; Lower panel: Variation in total phosphorous concentration across sites (surface and bottom data pooled); Boxplots are defined by minimum, median and maximum values (lines); 20th and 80th percentiles (boxes); and means (crosshairs). MFDP abbreviations: DC = D’Entrecasteaux Channel, PE = Port Esperance.


48

4.3.3 Phytoplankton 4.3.3.1 Chlorophyll a Chlorophyll a patterns were characterised by peaks in spring and autumn in most years, with seasonal minimums occurring in winter each year (Figure 23). The highest average chlorophyll a concentration during the 2012/13-2016/17 reporting period occurred in September 2015, when chlorophyll a averaged 3.5 mg/m3 across all sites. Across all sampling years, chlorophyll a concentrations tend to be higher and more variable at the Huon River sites in comparison with the D’Entrecasteaux Channel and control sites (Figure 23). Average chlorophyll a was lowest at control site 15, although occasional relatively high chlorophyll a concentrations were also measured at this site. Chlorophyll a patterns also tended to be less variable at control site 15 compared to remaining sites (Figure 23). There was no evidence of increasing chlorophyll a concentrations over the reporting period, nor was there evidence that the frequency and/or magnitude of bloom events has changed. Detailed chlorophyll a data for each site is included in Appendix 5.


49

Figure 23 Spatial and temporal variation in chlorophyll a concentration (mg/m3) from integrated samples (12 m). Upper panel: Mean monthly chlorophyll concentration from March 2009 to February 2017; Mid-panels: Variation in total chlorophyll concentration across sampling months; Lower panels: Variation in total chlorophyll concentration across sites; Boxplots are defined by minimum, median and maximum values (lines); 20th and 80th percentiles (boxes); and means (crosshairs). MFDP abbreviations: DC = D’Entrecasteaux Channel, PE = Port Esperance. Outliers are represented by the black circles in the upper portion of each box plot.


50

4.3.3.2 Species abundance patterns Patterns of phytoplankton abundance, as measured by cell counts are depicted in Figure 24. As expected, the highest peaks or blooms of phytoplankton abundance tended to occur during spring and/or autumn for most survey years (Figure 24). There were occasional exceptions to this general pattern. For example, in autumn and spring 2014 phytoplankton abundance was considerably lower than other survey years (Figure 24). Based on the cell count data, there was no evidence of an increase in the frequency or intensity of phytoplankton bloom events over the reporting period (Figure 24). Based on cell count data, the intensity of phytoplankton blooms (as measured by peaks in cell counts) tended to decline in the latter part of the reporting period (i.e. 2014/15 onwards; Figure 24).

When cell count data was pooled across all sites, the community has been clearly dominated by diatoms for all survey years. Relatively minor peaks in abundance of other phytoplankton groups have been occasionally recorded (e.g. prymnesiophytes during autumn 2009; dinoflagellates during autumn 2011; see Figure 24).

4.3.2.3 Harmful algal species The plankton dataset was also analysed to describe the abundance of species that are known to

form harmful algal blooms (HABs). For the purpose of this analysis, harmful algal species included

those with demonstrated impacts on aquaculture, human health and the environment. The harmful

species considered in the analysis species included species identified from the literature (Hallegraeff

2002), along with input from recognised phytoplankton experts. The abundance of known harmful

species was found to be very low across the survey period (Figure 35). An exception to this pattern

occurred during autumn 2011 (Year 3), when relative abundance of harmful species was high. This

was a result of a bloom of the dinoflagellate Gymnodinium catenatum. Overall, there was no

evidence of increasing abundance of harmful species during the survey period (Figure 25).

While the above analyses provided a useful depiction of potentially harmful species, it should be

noted that blooms of phytoplankton that are not normally considered harmful have the potential

to cause ecological harm when present in high densities (Smayda 2004). For example, diatoms are

not usually included among harmful phytoplankton groups but they have been implicated in causing

mortality and physiological impairment of farmed fish as a result of non-toxic stress (Smayda 2004).

Such adverse effects are most often related to morphological features of diatoms or to their

abundance (Smayda 2004).


51

Figure 24 Abundance of phytoplankton groups between March 2009 and February 2017. Data represent mean cell counts/mL across all sites for each sampling event.


52

Figure 25 Relative abundance of harmful and non-harmful algal species between March 2009 and February 2017. Data represent mean cell counts/mL across all sites for each sampling event


53

4.3.2.3 Phytoplankton communities

Analysis of phytoplankton abundance at the functional group level showed variation between regions and years. Consistent with the patterns described above, diatoms were the dominant group across all regions and years (Figure 26). Chaetoceros, Pseudo-nitzschia and Skeletonema were the most common genera recorded over the reporting period, although their relative abundance fluctuated between survey years (Figure 27). Average cell densities across all groups tended to be lowest at the control site 15, with abundance patterns more variable between years in the Huon and D'Entrecasteaux regions (Figure 26). Note that patterns of phytoplankton abundance at the functional group level for individual sites are summarised in Appendix 6.

Figure 26 Abundance of phytoplankton groups across sampling years for the D’Entrecasteaux, Huon and control sites (Note: control = 1 site; D’Entrecasteaux = 9 sites; Huon = 5 sites).

Figure 27 Relative abundance of diatom genera (Bacilliarophyta) across sampling years.


54

4.4 Comparison with proposed Trigger Values – Water Quality As outlined for sediment assessment, proposed baseline trigger levels established by Thompson et

al. (2008) provide a framework for developing management responses based on guideline or trigger

values (see Table 9). Proposed trigger levels are not statutory limits and their purpose is to inform

regulatory management of the industry. It is expected that EPA will be reviewing and updating

guideline/trigger values used in BEMP assessments.

Table 9 Standard or baseline values proposed for relevant water quality parameters – adapted from Thompson et al. (2008).

Parameter Standard or Baseline Value Level 1

(Low risk)

Level 2

(Moderate risk)

Level 3

(High risk) Huon Estuary D’Entrecasteaux

Channel

Nutrients1 Summer NH4+

CSIRO:

Surface = 0.32 μM.

Bottom = 0.42 μM

AST converted

(ammoniacal nitrogen):

Surface = 0.009 mg-N/L

Bottom = 0.011 mg-N/L

Summer NH4+

CSIRO

Surface = 0.12 μM.

Bottom = 0.27 μM

AST converted

(ammoniacal nitrogen):

Surface = 0.006 mg-N/L

Bottom = 0.009 mg-N/L

summer mean up

25%, or 3

successive annual

means >

baseline, or

mean for any one

site +50%

summer mean up

50%, or 8/10

annual means >

baseline for any

site, or mean for

any single site up

200%

Summer

mean +100%,

or summer

mean > 1 μM

(~ ANZECC)

Chlorophyll a sites 10 to 14 annual = 1.4

μg/L. Summer = 1.7 μg/L

Sites 1 to 9 summer

mean = 0.66 μg/L.

Annual mean = 0.80

μg/L

Any site: annual

mean +100%; or

average summer

mean +50%

Any site: annual

mean +200%; or

average summer

mean +100%; or

average annual

mean +50%

Any site:

annual mean

+400%; or

average

summer

mean +200%;

or average

annual mean

+100%

Phytoplankton

blooms

7% obs. > 3x median chl a 3.6% obs. > 3x median

chl a

% obs. > 3x

median rise 50%

% obs. > 3x

median rise 100%

% obs. > 3x

median rise

200%

Absolute DO2 Channel mean > 6 ppm.

Bay mean > 5 ppm

Channel mean > 6 ppm.

Bay mean > 5 ppm

Any 2 channel

observations ≤ 6

ppm. Any 2 bay

observations ≤ 5

ppm

50% of channel

observations ≤ 6

ppm. 50% of bay

observations ≤ 5

ppm. Any 2

observations < 2

ppm

Channel

mean ≤ 6

ppm. Bay

mean ≤ 5

ppm. Any 2

measurement

s < 1 ppm

Relative DO2

(percent

saturation)

Set at 20th percentile from

1st year of observations

Set at 20th percentile

from 1st year of

observations

Number of

observations

below baseline

increases 50%

Number of

observations

below baseline

increases 100%

Mean falls

10% from

baseline (~

ANZECC)

1Note that ammonium baseline values were originally based on CSIRO analyses. Since the BEMP data analysis used AST data (total ammoniacal nitrogen), these values required conversion. Conversion of these values was undertaken by IMAS and took account of comparative data from inter-laboratory analyses. See Appendix 7 for details. 2Note that while not explicitly stated in the in Thomson et al. (2008) table, dissolved oxygen values were examined against bottom water values – it was not meaningful to examine surface oxygen levels since these remain high even under conditions of high organic loading.


55

4.4.1 Nutrients – ammonia (total ammoniacal nitrogen) The concentration of ammonia was included as an important indicator of environmental condition (Thompson et al. 2008). Elevated ammonia levels are characteristic of organically enriched systems and indicate a failure of the system to effectively process nitrogen (Ross and Macleod 2013). It should be noted that there is some ambiguity in the trigger level criteria at the site level for nutrients, for the purpose of this report summer means were used. When mean values were considered across all sites, no trigger levels were reached for surface samples (Figure 28; Table 10). For bottom waters at D’Entrecasteaux Channel sites, the low risk level 1 (i.e. summer mean +25%) was reached in the 2014/15 sampling year. For the Huon MFDP2, the moderate risk level 2 was reached in 2009/10 and 2014/15, when the summer means were 50% greater than baseline values. At the individual site level for the D’Entrecasteaux Channel, (Figure 29), level 1 (low risk) levels were reached for summer mean values in bottom waters for at least one site in 2012/13, 2014/15, 2015/16 and 2016/17. Exceedances were most common at site 9 and site 8. Based on annual mean data, the low level risk level 1 was reached for site 2 in 2009 and site 9 for 2015/16 and 2016/17. For the Huon sites, level 1 (low risk) levels were reached for summer mean values in bottom waters for at least one site in all sampling years, with the exceedances most common at site 10. Based on summer mean values, site 10 also exceeded the level 2 (moderate risk) criteria, with a 200% increase observed in 2014/15. Overall, while there were numerous instances of nutrient trigger values being reached, for the majority of sites there was no evidence of an increasing frequency of exceedances over the duration of the monitoring program. Exceptions to this general pattern were evident at sites 8 and 9 in the D’Entrecasteaux Channel and site 10 in the Huon. At these sites there was a tendency for an increased frequency of exceedances based on summer mean values. At site 10, summer mean ammonia values measured in 2014/15 were the highest recorded since the inception of the BEMP program. Although recent years have seen relatively high summer ammonia levels at site 10, it should be noted that similarly high values have been recorded previously (e.g. 2009/10).

2 Note that the Huon MFDP analysis also included site 12 which is located in the Port Esperance MFDP


56

Figure 28 Summer and annual average ammonia concentrations measured during the BEMP program against the proposed baseline (black line) and 3 trigger levels (dashed horizontal lines +25%, +50%, +100%) in the D’Entrecasteaux Channel (upper panel) and Huon Estuary (lower panel).


57

Figure 29 Average ammonia concentrations over summer for individual sites showing the proposed baseline (black line) and 2 trigger levels (dashed horizontal lines, level 1 +50%, level 2 +200%) in the D’Entrecasteaux Channel (upper panels) and Huon Estuary (lower panels).


58

Table 10 – Summary of trigger level comparisons for ammonia. N = trigger level not reached; yellow = level 1 (low risk, i.e. summer mean up 25%, or 3 successive annual means > baseline, or mean for any site +50%), green = level 2 (moderate risk, i.e. summer mean up 50%, or 8/10 annual means > baseline for any site, or mean for any site + 200%), orange = level 3 (high risk, summer mean up 100%). Depth: S = surface; B = bottom. Note that for individual sites, the level presented is the maximum risk level observed across all sites for each MFDP.

MFDP and Criteria

Trigger level exceedances

20

09

/10

20

10

/11

20

11

/12

20

12

/13

20

13

/14

20

14

/15

20

15

/16

20

16

/17

Depth

S B S B S B S B S B S B S B S B

D’Entrecasteaux Channel

Summer mean N N N N N N N N N N N 1 N N N N

Annual mean N N N N N N N N N N N N N N N N

Individual sites (summer mean) N N N N N N N 1 N N 1 1 N 1 N 1

Huon

Summer mean N 2 N 1 N 1 N N N N N 2 N N N 1

Annual mean N N N N N 1 N 1 N N N N N N N N

Individual sites (summer mean) N 1 N 1 N 1 N 1 N 1 N 2 N 1 N 1

4.4.2 Chlorophyll/algal blooms Comparison of chlorophyll patterns against proposed baseline and trigger levels are displayed in Figure 30 and Figure 31 and summarised in Tables 11 and 12 below. Proposed trigger levels for chlorophyll a are based on values for individual sites and means across MFDP’s, as detailed in Thompson et al. 2008 (see Table 9 above). For the 2012-13-2016-17 reporting period at individual D’Entrecasteaux Channel and Huon sites, there were 7 instances of the level 1 trigger (i.e. annual mean +100%) being reached. This occurred at sites 1, 3 and 4, 10, 12 in 2012/13, site 4 in 2013/14 and site 11 in 2014/15. When average values across the MFDP’s were considered for the 2012/13-2016/17 reporting period there were four level 2 (moderate risk, i.e. summer mean + 100% or annual mean +50%) and three level 1 (low risk, i.e. summer mean +50%) exceedances evident. Average chlorophyll a reached level 2 (moderate risk) in 2012/13 for D’Entrecasteaux Channel based on annual means in 2012/13 and 2016/17, and also for summer mean values measured in 2012/13. Based on summer mean values, level 1 (low risk) was also reached in 2014/15 and 2016/17 for D’Entrecasteaux Channel sites. For the Huon MFDP, level 2 (moderate risk) was reached in 2012/13 based on annual means, while level 1 (low risk) was reached in 2016/17 based on summer mean values. When all survey years were considered, there was no indication of an increasing trend in the frequency of trigger levels being reached (Table 11, Table 12). Exceedances of proposed trigger levels appear linked to seasonal phytoplankton blooms which vary considerably in their timing, frequency and intensity. The phytoplankton bloom evident in autumn 2011, in particular, is reflected in a relatively high number of exceedances, including instances of level 3 (high risk) being reached. As noted in section 4.3.3, there was no evidence that the frequency and intensity of bloom events has increased since the inception of the monitoring program.


59

It is notable that trigger level exceedances were recorded for summer means. Given that phytoplankton blooms tend to occur naturally over the spring and autumn periods, slight variation in the timing of these blooms could have a substantial influence on summer mean values and interpretation of these levels. The proposed chlorophyll trigger values are also considered very complex to apply and interpret, since they incorporate specific sites as well as MFDP areas. As part of the review of trigger levels planned by the EPA, consideration of the approach to analysis of chlorophyll is recommended. Table 11 Maximum yearly exceedance level for annual chlorophyll for individual sites in the D’Entrecasteaux and Huon MFDP. N = trigger level not reached; yellow = level 1 (annual mean +100%), green = level 2 (annual mean +200%), orange = level 3 (annual mean +400%). Baseline values for sites were sourced from Thompson et al 2008.

MFDP and site Annual mean

(mg/m3)

20

09

/10

20

10

/11

20

11

/12

20

12

/13

20

13

/14

20

14

/15

20

15

/16

20

16

/17


1 0.9 N N 1 1 N N N N

2 0.85 N N N N N N N N

3 0.65 1 N 1 1 N N N N

4 0.68 N N 1 1 1 N N N

5 0.72 N N 1 N N N N N

6 0.79 N N 1 1 N N N N

7 0.92 N N 1 N N N N N

8 0.79 N N 3 N N N N N

9 0.92 N N 1 N N N N N

Huon

10 0.97 N N 3 1 N N N N

11 0.98 N N 3 1 N 1 N N

12 1.2 N N 1 N N N N N

13 2.2 N N N N N N N N

14 1.5 N N 1 N N N N N

Table 12 – Summary of trigger level comparisons for chlorophyll a based on average summer and annual values for the D’Entrecasteaux Channel and Huon MFDP’s. N = trigger level not reached; yellow = level 1 (average summer mean +50%), green = level 2 (Average summer mean +100%; or Average annual mean +50%), orange = level 3 (Average summer mean +200%; or average annual mean +100%). Baseline average values were sourced from Thompson et al 2008.

MFDP Mean (mg/m3)

20

09

/10

20

10

/11

20

11

/12

20

12

/13

20

13

/14

20

14

/15

20

15

/16

20

16

/17


Annual 0.80 2 N 3 2 N N N 2

Summer 0.66 N N 2 2 N 1 N 1

Huon

Annual 1.4 N N 3 2 N N N N

Summer 1.7 N N N N N N N 1


60

Figure 30 Mean summer and annual average chlorophyll a concentrations at each site measured during the BEMP program.


61

Figure 31 Annual and summer average chlorophyll a concentrations measured during the BEMP compared to proposed baseline and trigger levels in the D’Entrecasteaux Channel (top panel) and Huon Estuary (bottom panel). Baseline annual values represented by blue line; dashed blue lines represent +50 (level 2 moderate risk) and +100% (level 3 high risk) relative to baseline values. Baseline summer values represented by red line; dashed red lines represent +50 (level 1 low risk), +100% (level 2 moderate risk) and +200% (level 3 high risk) relative to baseline values.


62

4.4.3 Phytoplankton blooms

The baseline for phytoplankton bloom frequency was defined as 3.6 % and 7% of observations exceeding three times the median concentration for the D’Entrecasteaux Channel the Huon and regions respectively (Thompson et al. 2008). Trigger levels and performance based on these values are summarised in Table 13 below. For the 2012/13-2016/17 reporting period there was one instance of a trigger value being reached, when the level 2 trigger was exceeded for the Huon region in 2012/13 (Table 13). It is notable that in 2012/13 mean chlorophyll values were not unusually high (see Figure 23), however, over this period there were consecutive bloom events in both spring 2012 and the following autumn (2013). Table 13 Calculation of summary statistics and bloom frequency from integrated chlorophyll-a samples collected during the BEMP period, March 2009 – Feb 2017 in the D’Entrecasteaux Channel and Huon MFDP areas. Examples where trigger values are reached during the reporting period are highlighted in green, past exceedances are highlighted in yellow.

Trigger levels D’Entrecasteaux Channel Huon

Median chlorophyll a (µg/L) 1 1.2

3 x median (µg/L) 3 3.6

Total observations/year 135 75

Baseline bloom frequency 3.6% observations exceed median 7% observations exceed median

Level 1 5.4 % observations exceed median 10.5 % observations exceed median

Level 2 7.2% observations exceed median 14% observations exceed median

Level 3 14.4% observations exceed median 21% observations exceed median

Summary Data

2009/10 (% 3 x median) 3.7 4.0

2010/11 (% 3 x median) 0.7 9.3

2011/12 (% 3 x median) 8.1 10.7

2012/13 (% 3 x median) 2.2 20.0

2013/14 (% 3 x median) 0 1.3

2014/15 (% 3 x median) 0 8

2015/16 (% 3 x median) 3.7 8

2016/17 (% 3 x median) 1.5 4

4.4.4 Dissolved oxygen (absolute) A summary of absolute dissolved oxygen levels against proposed baseline and trigger levels are shown in Figure 32 and Table 14 below. For the D’Entrecasteaux Channel sites for the 2012/13-2016/17 reporting period, there were no instances of absolute dissolved oxygen concentration below the baseline and none of the risk levels identified in Thomson et al. (2008) were reached. For the Huon sites level 1 (low risk; any 2 channel observations ≤ 6 ppm; any 2 bay observations ≤ 5 ppm) was reached in most years (Table 14). There was no evidence of an increasing trend in the number of observations exceeding the baseline values for either of the sampling regions.


63

Figure 32 Bottom water dissolved oxygen concentrations (mg/L) measured during the BEMP program against the proposed baselines for bay and channel sites in the D’Entrecasteaux Channel (upper panel) and Huon (lower panel). Oxygen (mg/l). Black dashed lines = 1 ppm, 2 ppm; red dashed line = 5 ppm; blue dashed line = 6 ppm.


64

Table 14 Total number of observations and number of observations below the proposed baseline values of absolute concentrations of bottom water dissolved oxygen (mg/L) since 2009.

MFDP D’Entrecasteaux Channel Huon

Bay/Channel Bay Channel Bay Channel

Proposed baseline value ≤ 5 mg/L ≤ 6 mg/L ≤ 5 mg/L ≤ 6 mg/L

Total observations/year* 60 75 30 45

Summary Data

2009/10 No. observations ≤ 0 1 2 14








*Note these values represent the number of samples in most sample years. There were occasional years where these values varied slightly different (e.g. if there was a problem with the field measurement on a particular sampling occasion).

4.4.5 Dissolved oxygen (saturation)

A summary of dissolved oxygen saturation against proposed baseline and trigger levels are shown in Figure 33 and Table 15 below. For the proposed trigger levels the baseline was set at the 20th percentile of % saturation measurements from the first year of sampling and a level 1 (low risk) level was defined as a 50% increase from the baseline. The level 1 (low risk) trigger was not reached during the reporting period in channel or bay sites in either the D’Entrecasteaux Channel or Huon. There was also no evidence of an increasing trend in dissolved oxygen saturation levels below the baseline level of the duration of the BEMP program.


65

Figure 33 Bottom water dissolved oxygen concentration saturation (%) measured during the BEMP program against the proposed baselines for bay and channel sites in the D’Entrecasteaux Channel (upper panel) and Huon (lower panel). Blue dashed line = 20th percentile - Bay; red dashed line = 20th percentile - Channel.


66

Table 15 20th percentile of bottom water dissolved oxygen (% saturation) from 1st year of observations (i.e. 2009/10) and number of observations below the proposed baseline in each year.

MFDP D’Entrecasteaux Channel

Huon

Bay/Channel Bay Channel Bay Channel

2009/10 20th percentile (first year) 82.5 85.6 70.9 70.7

No. observations per year 60 75 60 90

Summary Data

2009/10 no. observations < 20th percentile 10 15 6 9









67

4.5. Quality Assurance Tables 16 and 17 below summarise QA/QC duplicate and field/trip blank comparisons. Although the 3BEMP schedule includes % variation to compare samples, the minimum reporting limit (MRL) was instead used for comparative purposes. MRL is a more informative measure for comparisons involving low concentrations of nutrients, which was the case for most analytes in the BEMP program. It should be noted that the MRL for some AST analytes changed during the reporting period. The analytes and MRL changes are included in the summary tables. For the duplicate samples, the proportion of samples varying by more than the MRL decline substantially following the change in laboratory reporting limits. Similarly, the proportion of field and trip blanks varying by a magnitude greater than the reporting limit also declined following the MRL change. Overall, there were no areas of concern in relation to QA/QC analyses. Detailed plots for each analyte are included for duplicates in Appendix 8 and field trip blank comparisons in Appendix 9. Table 16–QA duplicate sample results where differences were less than or greater than the minimum reporting limit. Note MRL for Nitrate, Silicate and Chlorophyll a remained unchanged over surveys 51-121. The QA/QC samples incorporated 71 sampling events from May 2012-Februaryu 2017

Analyte Criteria (±) Depth

% duplicate samples where difference between samples exceeded MRL

Overall May 2012-April 2014

May 2014-February 2017

Ammonia MRL

(0.002/0.005)

Surface 2.8 6.7 0

Bottom 1.4 0 2.4

Nitrate MRL (0.002) Surface 1.4 3.3 0

Bottom 4.2 3.3 9.8

Phosphate MRL

(0.002/0.003)

Surface 7 6.7 0

Bottom 2.8 3.3 2.4

Total Nitrogen MRL (0.04/0.1) Surface 16.9 40 0

Bottom 18.3 43.3 0

Total Phosphorus MRL

(0.005/0.001)

Surface 12.3 33.3 0

Bottom 19.7 43.3 2.4

Silicate MRL (0.2) Surface 1.4 0 2.4

Bottom 2.8 3.3 2.4

Chlorophyll a MRL (0.5) Integrated 1.4 3.3 0


68

Table 17– QA Trip and Field blank sample results where differences were greater than the MRL. Not MRL for nitrate and silicate remained unchanged over the survey period. The QA/QC samples incorporated 71 sampling events from May 2012-February 2017.

Analyte Criteria (±)

% sampling events where difference between trip and field blanks exceeded MRL

Overall May 2012-April 2014

May 2014-February 2017

Ammonia MRL

(0.002/0.005) 1.4 3.3 0

Nitrate MRL (0.002) 4.3 6.7 2.5

Phosphate MRL

(0.002/0.003) 1.4 3.3 0

Total Nitrogen MRL (0.04/0.1) 17.1 43.3 0

Total Phosphorus MRL

(0.005/0.001) 10 20 2.5

Silicate MRL (0.2) 0 0 0


69

5. References Birchenough, S. N. R., R. E. Parker, et al. (2012) "Combining bioturbation and redox metrics: Potential tools for assessing seabed function." Ecological Indicators 12(1): 8-16. Butler, E., Parslow, J., Volkman, J., Blackburn, S., Morgan, P., Hunter, J., Clementson, L., Parker, N., Bailey, R., Berry, K., Bonham, P., Featherstone, A., Griffin, D., Higgins, H., Holdsworth, D., Latham, V., Leeming, R., McGhie, T., McKenzie, D., Plaschke, R., Revill, A., Sherlock, M., Trenerry, L., Turnbull, A., Watson, R., and Wilkes, L. (2000) Huon Estuary Study – environmental research for integrated catchment management and aquaculture. Final report to Fisheries Research and Development Corporation. Project number 96/284. June 2000. CSIRO Division of Marine Research, Marine Laboratories, Hobart. Clarke, K.R. (1993) Non-parametric multivariate analyses of changes in community structure.

Australian Journal of Ecology 18: 117-143.

Clarke, K.R. & Gorley, R.N. (2001) PRIMER v5: User Manual/Tutorial PRIMER-E: Plymouth

Eriksen, R., Woods, G. Macleod, C. (2009) Inter-laboratory comparison of filtered and total nutrients, with emphasis on ammonia + ammonium. TAFI internal report, 28pp. Faith, D.P., Minchin, P.R. & Belbin, L. (1987) Compositional dissimilarity as a robust measure of

ecological distance. Vegetatio 69: 57-68.

Gibson, R. N., et al.(2011)"The use of sediment profile imaging (SPI) for environmental impact assessments and monitoring studies: lessons learned from the past four decades." Oceanography and Marine Biology: An Annual Review 49 (2011): 235-298. Hallegraeff, G.M. (2002) Aquaculturists’ Guide to Harmful Australian Microalgae, School of Plant Science, University of Tasmania, 136pp. Macleod, C.K. and Forbes, S. (2004) Guide to the assessment of sediment condition at marine finfish farms in Tasmania. Tasmanian Aquaculture and Fisheries Institute – University of Tasmania, Hobart, Australia, 65 pp. Ross, D. J. and Macleod, C. K. (2013) Evaluation of Broadscale Environmental Monitoring Program (BEMP) data from 2009-2012. IMAS Technical Report 140pp. Smayda, T. (2004) Harmful Algal Bloom Communities in Scottish Coastal Waters: Relationship to Fish Farming and Regional Comparisons – A Review February 2006 Paper 2006/3, 224pp. Thompson,P., Wild-Allen, K., Macleod, C., Swadling, K., Blackburn, S., and Volkman, J. (2008). Monitoring the Huon Estuary and D’Entrecasteaux Channel of the Environmental Effects of Finfish Aquaculture. Aquafin CRC Technical Report (CRC Project 4.2(2)/ FRDC Project 2004/074), Tasmanian Aquaculture & Fisheries Institute, Hobart, Tasmania, Australia Volkman, J. K., Thompson, P., Herzfeld, M., Wild-Allen, K., Blackburn, S., Macleod, C., Swadling, K., Foster, S., Bonham, P., Holdsworth, D., Clementson, L., Skerratt, J., Rosebrock, U., Andrewartha, and Revill, A. (2009) A whole-of-ecosystem assessment of environmental issues for salmonid


70

aquaculture. Aquafin CRC Project 4.2(2) (FRDC Project No. 2004/074). Aquafin Cooperative Research Centre, Fisheries Research and Development Corporation, Commonwealth Scientific and Industrial Research Organisation. Published by CSIRO Marine and Atmospheric Research


71

Appendix 1 (a) Sediment core descriptions 2012




B1.1 170 Dark grey

(10YR/4/1) Fine sand 20 Dark grey

(10YR/4/1) Fine sand and

shell grit 170 nil

Burrows, screwshell at

150 mm nil nil

B1.2 155 Dark grey

(10YR/4/1) Very fine sand 30 Dark grey


shell grit 155 nil

Burrows, screwshell at

130 mm nil nil

B1.3 105

Dark greyish brown



shell grit 105 nil

Burrows, screwshell at 80

mm nil nil

B2.1 200 Dark grey

(10YR/4/1) Very fine sand 200 nil Burrows nil nil

B2.2 210 Dark grey


B2.3 180 Dark grey

(10YR/4/1) Very fine sand 180 nil

Polychaete on sediment surface nil nil

B3.1 140

Very dark grey (10YR/3/1),

black streaks 40 - 120 mm

depth) Very fine sand and shell grit 140 nil Burrows nil nil

B3.2 140 Dark grey


B3.3 155 Dark grey

(10YR/4/1) Very fine sand and shell grit 155 nil Burrows nil nil

B4.1 150 Dark grey


B4.2 110 Dark grey

(10YR/4/1) Very fine sand 10

Very dark grey


shell grit 110 nil Burrows nil nil

B4.3 140 Dark grey



shell grit 140 nil nil nil nil


72




B5.1 130 Dark grey


B5.2 180 Dark grey



shell grit 180 nil

Burrows, ghost shrimp at 60

mm nil nil

B5.3 140 Dark grey




B6.1 150 Dark grey


B6.2 200 Dark grey

(10YR/4/1) Fine sand 200 nil

Worm tube on sediment surface nil nil

B6.3 170 Dark grey

(10YR/4/1) Very fine sand 170 nil nil nil nil

B7.1 175 Dark grey


B7.2 150 Dark grey


B7.3 200 Dark grey


B8.1 220 Dark grey


B8.2 160 Dark grey


B8.3 210 Dark grey


Burrows, worm in burrow at 80

mm nil nil

B9.1 180 Dark grey

(10YR/4/1) Fine sand 180 nil nil nil nil

B9.2 105 Dark grey


(10YR/4/1) Fine sand 105 nil Burrows nil nil

B9.3 185 Dark grey



73




B10.1 170


black streaks 30 - 120 mm Very fine sand 170 nil nil nil nil

B10.2 190


black streaks 0 - 40mm Very fine sand 190 nil Burrows nil nil

B10.3 210


darker streaks at 40 mm Very fine sand 210 nil Burrows nil nil

B11.1 190 Very dark grey






B12.1 200 Dark grey


B12.2 205

Dark grey (10YR/4/1), dark streaks

150 - 200 mm Very fine sand 205 nil nil nil nil

B12.3 195 Dark grey









(10YR/3/1) Very fine sand 180 nil Ghost shrimp at

90 mm nil nil


74








Burrows, ghost shrimp at 70

mm nil nil

B15.1 180

Dark grey (10YR/4/1), some dark streaks at bottom of

core Fine sand 180 nil

Polychaete on sediment surface nil nil

B15.2 180

Dark grey (10YR/4/1), some dark streaks at bottom of

core Fine sand 180 nil

Burrows, polychaete at 80

mm nil nil

B15.3 170 Dark grey

(10YR/4/1) Fine sand, shell grit at 145 mm 170 nil nil nil nil


75

Appendix 1 (b) Sediment core descriptions 2013




B1.1 100 Grey

(10YR/5/1) Very fine sand 40 Grey



B1.2 170 Dark grey




B1.3 100 Grey


(10YR/4/1)

Fine sand and shell grit, large

screwshells 100 nil

Decorator crab, screwshells at

50 mm nil nil

B2.1 190 Dark grey


B2.2 200 Dark grey


B2.3 100 Dark grey


B3.1 190 Dark grey


B3.2 120 Dark grey


B3.3 195 Dark grey


B4.1 170 Dark grey



B4.2 170 Dark grey




B4.3 125 Dark grey



B5.1 175 Dark grey

(10YR/4/1) Very fine sand and shell grit 175 nil

Burrows, decorator crab nil nil

B5.2 110 Dark grey


B5.3 150 Dark grey



76




B6.1 130 Dark grey



Burrows, screwshells at

120 mm nil nil

B6.2 105 Dark grey


B6.3 160 Dark grey


B7.1 185 Dark grey


B7.2 160 Dark grey


B7.3 190

Dark grey (10YR/4/1),

black streaks at 30 mm Very fine sand 190 nil Burrows nil nil

B8.1 190 Dark grey

(10YR/4/1) Very fine sand 190 nil Burrows, squat

lobster nil nil

B8.2 180 Dark grey

(10YR/4/1) Very fine sand 180 nil Burrows, squat

lobster nil nil

B8.3 190 Dark grey


B9.1 160 Dark grey


(10YR/4/1) Fine sand 160 nil nil nil nil

B9.2 120

Dark grey (10YR/4/1),

dark streak at 40 mm Fine sand 120 nil Hermit crab nil nil

B9.3 155 Dark grey



B10.1 135

Very dark grey (10YR/3/1), dark streaks 40 - 70 mm Very fine sand 135 nil Burrows nil nil


77




B10.2 190

Very dark grey (10YR/3/1), dark streaks 20 - 50 mm Very fine sand 190 nil Burrows nil nil

B10.3 175


darker streaks at 40 mm Very fine sand 175 nil Burrows nil nil







B12.1 200 Dark grey


B12.2 190 Dark grey


B12.3 180

Dark grey (10YR/4/1), feint dark

streak at 20 mm Very fine sand 180 nil Burrows nil nil


(10YR/3/1) Very fine sand 200 nil Single burrow at

10 mm nil nil



B13.3 190

Very dark grey (10YR/3/1), dark streaks 80 -180 mm Very fine sand 190 nil Burrows nil nil






78






B15.1 170

Dark grey (10YR/4/1), dark streaks

110 - 150 mm Very fine sand 2 Fine sand 170 nil Burrows nil nil

B15.2 150

Dark grey (10YR/4/1), dark streaks 70 - 100 mm Very fine sand 2 Fine sand 150 nil nil nil nil

B15.3 205 Dark grey

(10YR/4/1) Very fine sand 2

Fine sand, shell grit at

190 mm 205 nil Burrows nil nil


79

Appendix 1 (c) Sediment core descriptions 2014




B1.1 120 Dark grey



shell grit 120 nil

Burrows, ghost shrimp on sediment

surface, screw shells @ 70 mm nil nil

B1.2 140 Dark grey



B1.3 100 Dark grey


(10YR/4/1)

Fine sand and shell grit,

some large shell

fragments 100 nil Burrows,

polychaetes nil nil

B2.1 180 Dark grey


(10YR/4/1) nil Burrows nil nil

B2.2 180 Dark grey


(10YR/4/1) nil Burrows nil nil

B2.3 180 Dark grey


(10YR/4/1) nil

Burrows, ghost shrimp @ 150

mm nil nil

B3.1 170 Dark grey



mm nil nil

B3.2 150 Dark grey

(10YR/4/1) Very fine sand and shell grit 50

Dark grey (10YR/4/1) Very fine sand 150 nil

Burrows, polychaete on

sediment surface nil nil

B3.3 150 Dark grey



mm nil nil

B4.1 100 Dark grey



Burrows, bivalve on sediment

surface nil nil

B4.2 140 Dark grey



80




B4.3 120 Dark grey


(10YR/4/1) Very fine sand and shell grit 120 nil nil nil nil

B5.1 100 Dark grey





B5.2 110 Dark grey





B5.3 100 Dark grey



Burrows, polychaete on edge of core nil nil

B6.1 160 Dark grey


Burrows, amphipod on


B6.2 170 Dark grey



mm nil nil

B6.3 140 Dark grey


B7.1 200 Dark grey


B7.2 180 Dark grey


Burrows, polychaete @

100 mm nil nil

B7.3 190 Dark grey


B8.1 180 Dark grey


B8.2 200 Dark grey



81




B8.3 210 Dark grey



mm nil nil

B9.1 150 Dark grey



B9.2 180 Dark grey

(10YR/4/1) Fine sand 180 nil

Burrows, amphipod at


B9.3 160 Dark grey



B10.1 190 Dark grey


B10.2 190 Dark grey

(10YR/4/1) Silt 2 Dark grey


B10.3 110 Dark grey

(10YR/4/1) Silt 2 Dark grey




Burrows, squat lobster on sediment surface nil nil





B12.1 100 Dark grey


B12.2 120 Dark grey


B12.3 170 Dark grey







82






B14.1 180


dark streak at 170 mm Very fine sand 180 nil Burrows nil nil





B15.1 170 Dark grey


(10YR/4/1)

Fine sand, dark streaks 80 - 170 mm nil Burrows nil nil

B15.2 110 Dark grey


(10YR/4/1)


B15.3 130 Dark grey


(10YR/4/1)



83

Appendix 1 (d) Sediment core descriptions 2015

Core Length (mm)

Colour 1 Sediment 1 Depth 1 (mm)


Plants Animals Gas Smell

B1.1 160 10YR/5/1 Grey Very fine sand 30 10YR/5/1 Grey Fine sand and shell grit, large shell fragments

160 Nil Burrows, screw shell on sediment surface


130 Nil Burrows Nil Nil



B2.1 180 10YR/4/1 Dark grey

Very fine sand 180 Nil Burrows Nil Nil






Very fine sand and sparse shell grit









Very fine sand 5 10YR/4/1 Dark grey

Fine sand and shell grit

180 Nil Burrows, ghost shrimp at 30 mm

Nil Nil











100 10YR/4/1 Dark grey

Nil Burrows Nil Nil




Nil Burrows Nil Nil







84

Core Length (mm)






170 Nil

Burrows, worm tube on sediment surface, ghost shrimp at 90 mm

Nil Nil



140 Nil Nil Nil Nil





Very fine sand 180 Nil Burrows, polychaete on sediment surface

Nil Nil




Very fine sand 200 Nil Burrows, small crab on sediment surface

Nil Nil





Nil Nil



Nil Nil


Fine sand 160 Nil Burrows Nil Nil




Fine sand 130 Nil Burrows, worm tube on sediment surface

Nil Nil

B10.1 160 10YR/3/1 Very dark grey





85

Core Length (mm)












B12.1 200 10YR/4/1 Dark grey

Very fine sand 200 Nil

Burrows, polychaete at 120mm, ghost shrimp at 90 mm

Nil Nil

B12.2 150 10YR/4/1 Dark grey


B12.3 125 10YR/4/1 Dark grey


B13.1 130 10YR/2/1 Black Very fine sand 130 Nil

Burrows, polychaete at 50 mm amphipod at 50 mm

Nil Nil









B15.1 125

10YR/4/1 Dark grey, dark streaks 50-70 mm


B15.2 100 10YR/4/1 Dark grey, dark



86

Core Length (mm)




streaks 60-90 mm

B15.3 175

10YR/4/1 Dark grey, dark streaks 80-120 mm



87

Appendix 2 Stable isotope raw data

Sample No.

Year

2009 2013 2009 2013 2009 2013 2009 2013 2009 2013

d15

N ‰

AIR

(co

rr)

d15

N ‰

AIR

d13

C ‰

VP

DB

d13

C ‰

V

PD

B

N w

gt %

(car

bo

nat

e f

ree

)

N w

gt %

C w

gt %

(car

bo

nat

e f

ree

)

C w

gt %

C/N

*

C/N

mo

lar

IM1-1 sediment 8.29 8.73 -22.09 -22.09 0.43 0.34 3.75 2.80 10.17 9.61

IM1-2 sediment 8.52 6.93 -22.09 -22.06 0.53 0.15 4.76 1.21 10.48 9.41

IM1-3 sediment 10.88 7.03 -21.42 -22.24 1.20 0.34 7.47 2.82 7.26 9.68

IM2-1 sediment 7.77 6.96 -22.60 -22.74 0.43 0.21 4.20 2.18 11.40 12.11

IM2-2 sediment 7.39 6.32 -22.67 -22.61 0.43 0.21 4.15 2.70 11.26 15.00

IM2-3 sediment 7.65 7.19 -22.71 -22.58 0.39 0.20 3.79 2.16 11.34 12.60

IM3-1 sediment 7.48 10.20 -23.01 -22.28 0.22 0.10 2.06 1.02 10.92 11.90

IM3-2 sediment 7.96 8.91 -22.45 -20.37 0.16 0.08 1.47 0.87 10.72 12.69

IM3-3 sediment 7.84 7.44 -22.74 -22.97 0.22 0.13 1.99 1.23 10.55 11.04

IM4-1 sediment 7.29 10.16 -22.76 -19.40 0.14 0.06 1.28 0.68 10.67 13.22

IM4-2 sediment 6.85 8.74 -22.77 -22.20 0.09 0.05 0.89 0.46 11.54 10.73

IM4-3 sediment 7.27 9.47 -22.77 -22.06 0.06 0.05 0.56 0.46 10.89 10.73

IM5-1 sediment 8.24 7.41 -22.67 -21.00 0.26 0.16 2.71 1.87 12.16 13.64

IM5-2 sediment 8.15 6.31 -22.66 -23.51 0.36 0.14 3.68 1.54 11.93 12.83

IM5-3 sediment 7.63 7.11 -22.49 -22.46 0.38 0.23 2.78 2.38 8.54 12.07

IM6-1 sediment 7.63 7.24 -23.18 -22.13 0.09 0.11 0.80 1.18 10.37 12.52

IM6-2 sediment 7.21 8.72 -23.26 -22.91 0.08 0.04 0.73 0.48 10.65 14.00

IM6-3 sediment 6.78 7.15 -23.18 -22.97 0.07 0.05 0.63 0.57 10.50 13.30

IM7-1 sediment 8.47 8.49 -22.80 -23.12 0.39 0.34 3.76 3.54 11.25 12.15

IM7-2 sediment 8.72 7.69 -22.60 -22.89 0.42 0.32 4.47 3.22 12.42 11.74

IM7-3 sediment 8.84 8.27 -22.66 -22.93 0.38 0.31 3.76 3.24 11.54 12.19

IM8-1 sediment 9.19 8.02 -22.69 -22.69 0.23 0.26 2.22 2.68 11.26 12.03

IM8-2 sediment 8.13 7.77 -22.82 -22.79 0.12 0.27 1.15 2.69 11.18 11.62

IM8-3 sediment 8.24 7.23 -22.68 -22.96 0.18 0.22 1.69 2.33 10.95 12.36

IM9-1 sediment 6.88 2.76 -23.01 -23.57 0.07 0.04 0.40 0.36 6.62 9.85

IM9-2 sediment 7.96 8.35 -22.90 -23.31 0.08 0.07 0.62 0.80 9.10 9.58

IM9-3 sediment 8.18 5.52 -22.77 -24.33 0.07 0.04 0.22 0.47 3.67 9.17

IM10-1 sediment 8.47 7.65 -23.55 -23.59 0.51 0.28 5.65 3.19 12.92 13.29

IM10-2 sediment 8.17 7.38 -23.47 -23.53 0.49 0.36 5.36 3.89 12.76 12.61

IM10-3 sediment 8.00 7.59 -23.51 -24.01 0.51 0.28 5.71 3.23 13.06 13.46

IM11-1 sediment 7.19 6.62 -24.32 -24.44 0.45 0.28 6.22 3.40 16.13 14.17

IM11-2 sediment 6.79 5.99 -24.45 -24.22 0.42 0.21 6.27 2.85 17.42 15.83

IM11-3 sediment 7.64 7.16 -24.22 -24.20 0.46 0.29 6.03 3.57 15.29 14.36

IM12-1 sediment 8.00 8.48 -23.16 -23.20 0.55 0.41 6.16 4.03 13.07 11.47

IM12-2 sediment 7.93 7.28 -23.14 -22.89 0.52 0.40 5.77 4.08 12.95 11.90

IM12-3 sediment 7.98 7.60 -23.00 -23.09 0.54 0.38 5.77 3.81 12.47 11.70

IM13-1 sediment 3.67 3.75 -26.17 -27.78 0.47 0.20 11.18 5.32 27.75 31.03

IM13-2 sediment 3.69 3.60 -26.14 -27.40 0.44 0.38 10.78 8.25 28.58 25.33

IM13-3 sediment 3.39 0.77 -26.08 -27.83 0.46 0.18 10.96 4.58 27.80 29.69

IM14-1 sediment 6.23 5.42 -25.52 -26.86 0.45 0.28 7.25 4.55 18.80 18.96

IM14-2 sediment 5.49 6.18 -25.36 -24.59 0.47 0.36 8.05 5.61 19.98 18.18

IM14-3 sediment 6.18 5.61 -25.47 -26.26 0.49 0.19 7.88 3.68 18.76 22.60

IM15-1 sediment 6.93 7.50 -23.80 -22.68 0.07 0.05 0.60 0.43 10.00 10.03

IM15-2 sediment 7.94 7.87 -23.79 -23.61 0.12 0.04 1.01 0.37 9.82 10.79

IM15-3 sediment 7.69 7.98 -23.90 -22.29 0.08 0.06 0.74 0.64 10.79 12.44


88

Appendix 3 (a) Temporal variation in temperature (°C) at three depths (Surface, 5m, Bottom) for each site, March 2009-February 2017.


89

Appendix 3 (b) Temporal variation in salinity (ppt) at three depths (Surface, 5m, Bottom) for each site, March 2009-February 2017.


90

Appendix 3 (c) Temporal variation in absolute dissolved oxygen (mg/L) at three depths (Surface, 5m, Bottom) for each site, March 2009-February 2017.


91

Appendix 4 (a) Temporal variation in ammonia concentration (mg-N/L) at two depths (Surface, Bottom) for each site, March 2009-February 2017.


92

Appendix 4 (b) Temporal variation in nitrate concentration (mg-N/L) at two depths (Surface, Bottom) for each site, March 2009-February 2017.


93

Appendix 4 (c) Temporal variation in phosphate concentration (mg-P/L) at two depths (Surface, Bottom) for each site, March 2009-February 2017.


94

Appendix 4 (d) Temporal variation in silicate concentration (mg/L) at two depths (Surface, Bottom) for each site, March 2009-February 2017.


95

Appendix 4 (e) Temporal variation in total nitrogen concentration (mg-N/L) at two depths (Surface, Bottom) for each site, March 2009-February 2017.


96

Appendix 4 (f) Temporal variation in total phosphorous concentration (mg-P/L) at two depths (Surface, Bottom) for each site, March 2009-February 2017.


97

Appendix 5 Temporal variation in chlorophyll a concentration (mg/m3) for each site, March 2009-February 2017.


98

Appendix 6 (a) Abundance of phytoplankton between March 2009 and February 2017 at each site: Sites 1-3.

0%

10%

20%

30%

40%

50%

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70%

80%

90%

100%

20

09

/10

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% o

f m

ean

cel

ls/m

L/sa

mp

ling

even

t

Sampling year

Site 1

Raphidophyta

Prymnesiophyta

Euglenophyta

Dinophyta

Cryptophyta

Chrysophyta

Chlorophyta

Bacillariophyta

0%

10%

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100%

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t

Sampling year

Site 2

Raphidophyta

Prymnesiophyta

Euglenophyta

Dinophyta

Cryptophyta

Chrysophyta

Chlorophyta

Bacillariophyta

0%

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% o

f m

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cel

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mp

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even

t

Sampling year

Site 3

Raphidophyta

Prymnesiophyta

Euglenophyta

Dinophyta

Cryptophyta

Chrysophyta

Chlorophyta

Bacillariophyta


99

Appendix 6 (b) Abundance of phytoplankton between March 2009 and February 2017 at each site: Sites 4-6.

0%

10%

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100%

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mea

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ells

/mL/

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plin

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Sampling year

Site 4

Raphidophyta

Prymnesiophyta

Euglenophyta

Dinophyta

Cryptophyta

Chrysophyta

Chlorophyta

Bacillariophyta

0%

10%

20%

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100%

20

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Sampling year

Site 5

Raphidophyta

Prymnesiophyta

Euglenophyta

Dinophyta

Cryptophyta

Chrysophyta

Chlorophyta

Bacillariophyta

0%

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20

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Sampling year

Site 6

Raphidophyta

Prymnesiophyta

Euglenophyta

Dinophyta

Cryptophyta

Chrysophyta

Chlorophyta

Bacillariophyta


100

Appendix 6 (c) Abundance of phytoplankton between March 2009 and February 2017 at each site: Sites 7-9.

0%

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Sampling year

Site 7

Raphidophyta

Prymnesiophyta

Euglenophyta

Dinophyta

Cryptophyta

Chrysophyta

Chlorophyta

Bacillariophyta

0%

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Sampling year

Site 8

Raphidophyta

Prymnesiophyta

Euglenophyta

Dinophyta

Cryptophyta

Chrysophyta

Chlorophyta

Bacillariophyta

0%

10%

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50%

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100%

20

09

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Sampling year

Site 9

Raphidophyta

Prymnesiophyta

Euglenophyta

Dinophyta

Cryptophyta

Chrysophyta

Chlorophyta

Bacillariophyta


101

Appendix 6 (d) Abundance of phytoplankton between March 2009 and February 2017 at each site: Sites 10-12.

0%

10%

20%

30%

40%

50%

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100%

20

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Sampling year

Site 10

Raphidophyta

Prymnesiophyta

Euglenophyta

Dinophyta

Cryptophyta

Chrysophyta

Chlorophyta

Bacillariophyta

0%

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Sampling year

Site 11

Raphidophyta

Prymnesiophyta

Euglenophyta

Dinophyta

Cryptophyta

Chrysophyta

Chlorophyta

Bacillariophyta

0%

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20

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Sampling year

Site 12

Raphidophyta

Prymnesiophyta

Euglenophyta

Dinophyta

Cryptophyta

Chrysophyta

Chlorophyta

Bacillariophyta


102

Appendix 6 (e) Abundance of phytoplankton between March 2009 and February 2017 at each site: Sites 13-15.

0%

10%

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100%

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Site 13

Raphidophyta

Prymnesiophyta

Euglenophyta

Dinophyta

Cryptophyta

Chrysophyta

Chlorophyta

Bacillariophyta

0%

10%20%

30%40%

50%60%70%

80%

90%100%

20

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Sampling year

Site 14

Raphidophyta

Prymnesiophyta

Euglenophyta

Dinophyta

Cryptophyta

Chrysophyta

Chlorophyta

Bacillariophyta

0%

10%

20%

30%

40%

50%

60%

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80%

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100%

20

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ean

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mp

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t

Sampling year

Site 15

Raphidophyta

Prymnesiophyta

Euglenophyta

Dinophyta

Cryptophyta

Chrysophyta

Chlorophyta

Bacillariophyta


103

Appendix 7 Conversion of ammonia baseline levels from CSIRO to AST data. Details below were provided by IMAS.

Rationale

The initial analysis of dissolved nutrients for the BEMP was undertaken by CSIRO, and the draft

baselines and performance indicators were based on CSIRO measurements. Since June 2012 AST

has been contracted to analyse the dissolved nutrients. It is known from an interlaboratory

comparisons that there is some discrepancy in the measurement of ammonia concentration

between the laboratories. Fortunately, AST were contracted to measure total N and total P for the

entire BEMP monitoring period and, when measuring total N, also measured ammonia

concentration and provisioned this data for the current study. As such, ammonia data were available

from both AST and CSIRO for the first 51 BEMP surveys (June 2010 – May 2012). Using these data,

a linear model was developed to convert the baseline ammonia estimates proposed by Volkman et

al. (2009) (i.e. based on CSIRO measured ammonia) to values that align with AST measured

ammonia.

Correction for inter-laboratory variation in ammonia measurement As AST were able to provide ammonia concentrations for the first 51 BEMP campaigns, when

technically CSIRO were contracted to do so, it was not necessary to correct for inter-laboratory

variation in ammonia concentration reported by Eriksen (2009). It was, however, necessary to

correct for this difference to allow ammonia to be compared against the baselines and triggers that

were proposed by CSIRO using ammonia measurements undertaken in their laboratories

(Thompson et al., 2008).

Firstly, units were converted from μM-N to mg/l-N (hereafter abbreviated to mg/l) using its

molecular weight (14.0067 μ). To confirm the mean difference of 0.21 μM-N between CSIRO and

AST determined by Eriksen (2009), data from surveys 1– 51 when the laboratories were measuring

ammonia/ammonium concurrently, were compared. A linear relationship between the data sets

was identified and modelled (Figure A; Table A). The model provided a relatively good fit (R2 =

0.73). This indicates that the difference between the two laboratories is dependent on

concentration, and that using the modelled relationship would be more accurate method for

conversion than the offset of 0.21 μM-N determined by Eriksen (2009); this likely reflects the much

larger data set now available for the inter-laboratory comparison.


104

Figure A: Linear relationship between CSIRO and AST ammonia/ammonium N concentration.

Blue line indicates the linear relationship; shaded area represents 95% confidence intervals of

the model.

Table A: Linear model of CSIRO and AST ammonia/ammonium concentration to facilitate the

conversion of CSIRO data to align with the latter AST data.

Summary statistics are as follows: residual standard error = 0.003428 on 1086 degrees of freedom,

multiple R-squared = 0.7343, adjusted R-squared = 0.7373, F-statistic = 3004 on 1 and 1086 DF, p-

value = <0.001.

Coefficient Estimate Std. error t-value p

(Intercept) 0.0047481 0.0001298 36.57 <0.001 AST ammonia

1.0017627 0.0182764 54.81 <0.001


105

Appendix 8 QA/QC analyses – duplicate sample comparisons. Error bars indicate ± MRL values aligned with the sample value. MRL values are included at the bottom of each figure. Note that surveys 51-80 = May 2012-April 2014; surveys 81-121 = May 2014-February 2017.

±0.002(51-80)/0.005(81-121)

±0.002(51-80)/0.005(81-121)

±0.002

±0.002


106

±0.002(51-80)/0.003(81-121)

±0.002(51-80)/0.003(81-121)

±0.04(51-80)/0.1(81-121)

±0.04(51-80)/0.1(81-121)


107

±0.005(51-80)/0.01(81-121)

±0.005(51-80)/0.01(81-121)

±0.2

±0.2


108

±0.5


109

Appendix 9 QA/QC analyses – field and trip blank comparisons. Error bars indicate ± MRL values aligned with the trip blank value. MRL values are included at the bottom of each figure. Note that surveys 51-80 = May 2012-April 2014; surveys 81-121 = May 2014-February 2017.

±0.002(51-80)/0.005(81-121)

±0.002

±0.002(51-80)/0.003(81-121)

±0.04(51-80)/0.1(81-121)


110

±0.005(51-80)/0.01(81-121)

±0.2

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